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    Msx3 msh homeobox 3 [ Mus musculus (house mouse) ]

    Gene ID: 17703, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Msx3provided by MGI
    Official Full Name
    msh homeobox 3provided by MGI
    Primary source
    MGI:MGI:106587
    See related
    Ensembl:ENSMUSG00000025469 AllianceGenome:MGI:106587
    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
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within negative regulation of histone acetylation and negative regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including central nervous system; future hindbrain; genitourinary system; and trunk mesenchyme. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in CNS E11.5 (RPKM 2.6), CNS E14 (RPKM 0.6) and 4 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Msx3 in Genome Data Viewer
    Location:
    7 F4; 7 85.04 cM
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (139626070..139629001, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (140046157..140049088, complement)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene a disintegrin and metallopeptidase domain 8 Neighboring gene STARR-seq mESC enhancer starr_20441 Neighboring gene microRNA 7062 Neighboring gene tubulin, gamma complex component 2 Neighboring gene STARR-seq mESC enhancer starr_20442 Neighboring gene STARR-positive B cell enhancer ABC_E6615 Neighboring gene STARR-positive B cell enhancer ABC_E8219 Neighboring gene zinc finger protein 511 Neighboring gene VISTA enhancer mm1489 Neighboring gene STARR-seq mESC enhancer starr_20446 Neighboring gene calcyon neuron-specific vesicular protein Neighboring gene STARR-seq mESC enhancer starr_20447 Neighboring gene proline-rich acidic protein 1

    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. MSX3 Switches Microglia Polarization and Protects from Inflammation-Induced Demyelination. Yu Z, et al. J Neurosci, 2015 Apr 22. PMID 25904788, Free PMC Article
    2. Distinct activities of Msx1 and Msx3 in dorsal neural tube development. Liu Y, et al. Development, 2004 Mar. PMID 14973289
    3. Msx homeobox gene family and craniofacial development. Alappat S, et al. Cell Res, 2003 Dec. PMID 14728799
    4. The mechanism of biogenesis and potential function of the two alternatively spliced mRNAs encoded by the murine Msx3 gene. Matsui H, et al. Mol Cell Biochem, 2004 Dec. PMID 15663180
    5. The murine homeobox gene Msx-3 shows highly restricted expression in the developing neural tube. Shimeld SM, et al. Mech Dev, 1996 Apr. PMID 8861099

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. findings established MSX3 as an important microglia polarization regulator, suggested a previously unknown signaling mechanism of MSX3 function.
      Title: MSX3 Switches Microglia Polarization and Protects from Inflammation-Induced Demyelination.
    2. Msx1 and Msx3 can mediate distinct aspects of Bmp signaling during neural tube development
      Title: Distinct activities of Msx1 and Msx3 in dorsal neural tube development.
    3. The function of the two alternatively spliced mRNAs encoded by Msx3 was studied.
      Title: The mechanism of biogenesis and potential function of the two alternatively spliced mRNAs encoded by the murine Msx3 gene.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    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 MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone acetyltransferase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone acetyltransferase regulator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in embryonic morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    homeobox protein MSX-3
    Names
    homeo box, msh-like 3
    homeobox, msh-like 3

    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_001347609.1 → NP_001334538.1  homeobox protein MSX-3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC109205
      Consensus CDS
      CCDS85451.1
      UniProtKB/TrEMBL
      G3X9C7
      Related
      ENSMUSP00000057312.7, ENSMUST00000055353.9

    2. NM_010836.3 → NP_034966.1  homeobox protein MSX-3 isoform 1

      See identical proteins and their annotated locations for NP_034966.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK012556, BC051983
      Consensus CDS
      CCDS21961.1
      UniProtKB/Swiss-Prot
      P70246, P70354, Q03360, Q80W10
      UniProtKB/TrEMBL
      B2RPS3
      Related
      ENSMUSP00000133484.2, ENSMUST00000172775.4
      Conserved Domains (1) summary
      pfam00046
      Location:90 → 143
      Homeobox; Homeobox domain

    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_000073.7 Reference GRCm39 C57BL/6J

      Range
      139626070..139629001 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P70354.1 GenPept UniProtKB/Swiss-Prot:P70354

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