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

Gene ID: 16911, updated on 12-May-2024

Summary

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
Predicted to enable metal ion binding activity. Involved in positive regulation of kinase activity and regulation of cell migration. Acts upstream of or within several processes, including cell differentiation in spinal cord; neural tube closure; and thymus development. Located in cell leading edge and nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including branchial arch; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. Used to study anencephaly. Orthologous to human LMO4 (LIM domain only 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E18 (RPKM 58.7), cortex adult (RPKM 56.2) and 28 other tissues See more
Orthologs
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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

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_001161769.1NP_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:2377
    LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
    cd09387
    Location:87141
    LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)
  2. NM_001161770.1NP_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:2377
    LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
    cd09387
    Location:87141
    LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)
  3. NM_010723.3NP_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:2377
    LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
    cd09387
    Location:87141
    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)