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    Runx3 runt related transcription factor 3 [ Mus musculus (house mouse) ]

    Gene ID: 12399, updated on 9-Dec-2024

    Summary

    Official Symbol
    Runx3provided by MGI
    Official Full Name
    runt related transcription factor 3provided by MGI
    Primary source
    MGI:MGI:102672
    See related
    Ensembl:ENSMUSG00000070691 AllianceGenome:MGI:102672
    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
    Rx3; AML2; Cbfa3; Pebp2a3
    Summary
    Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including negative regulation of epithelial cell proliferation; negative regulation of transcription by RNA polymerase II; and regulation of alpha-beta T cell differentiation. Acts upstream of or within several processes, including chondrocyte differentiation; hair follicle morphogenesis; and positive regulation of extrinsic apoptotic signaling pathway. Located in chromatin and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; limb; nervous system; and sensory organ. Used to study asthma; idiopathic scoliosis; and inflammatory bowel disease. Human ortholog(s) of this gene implicated in several diseases, including breast cancer (multiple); female reproductive organ cancer (multiple); lung non-small cell carcinoma; pancreatic cancer; and urinary bladder cancer. Orthologous to human RUNX3 (RUNX family transcription factor 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in spleen adult (RPKM 11.1), thymus adult (RPKM 6.0) and 11 other tissues See more
    Orthologs
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    Genomic context

    See Runx3 in Genome Data Viewer
    Location:
    4 D3; 4 67.19 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (134847956..134905301)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (135120645..135177990)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene DRG (dorsal root ganglion) regulatory region upstream of Runx3 Neighboring gene predicted gene, 42327 Neighboring gene STARR-positive B cell enhancer ABC_E6232 Neighboring gene predicted gene 16225 Neighboring gene STARR-positive B cell enhancer ABC_E1659 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:134762237-134762420 Neighboring gene STARR-positive B cell enhancer mm9_chr4:134781869-134782170 Neighboring gene chloride intracellular channel 4 Neighboring gene STARR-positive B cell enhancer ABC_E3528 Neighboring gene STARR-positive B cell enhancer ABC_E7998 Neighboring gene VISTA enhancer mm1648 Neighboring gene STARR-positive B cell enhancer ABC_E524 Neighboring gene predicted gene, 30767

    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

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell maturation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in chondrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within chondrocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within hair follicle morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hemopoiesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of CD4-positive, alpha-beta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within neuron projection development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ossification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of CD8-positive, alpha-beta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of extrinsic apoptotic signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to transforming growth factor beta ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to transforming growth factor beta ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within type II interferon production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of core-binding factor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    runt-related transcription factor 3
    Names
    CBF-alpha-3
    PEA2-alpha C
    PEBP2-alpha C
    SL3-3 enhancer factor 1 alpha C subunit
    SL3/AKV core-binding factor alpha C subunit
    acute myeloid leukemia 2 protein
    core binding factor alpha 3
    core-binding factor subunit alpha-3
    oncogene AML-2
    polyomavirus enhancer-binding protein 2 alpha C subunit
    runt domain, alpha subunit 3
    transcription factor AML2/CBFA3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001369050.1NP_001355979.1  runt-related transcription factor 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL731718
      Consensus CDS
      CCDS89843.1
      UniProtKB/Swiss-Prot
      B2FDG4, Q64131, Q99P92, Q9R199
      Related
      ENSMUSP00000113159.2, ENSMUST00000119564.2
      Conserved Domains (2) summary
      pfam00853
      Location:63184
      Runt; Runt domain
      pfam08504
      Location:314409
      RunxI; Runx inhibition domain
    2. NM_019732.2NP_062706.2  runt-related transcription factor 3 isoform 1

      See identical proteins and their annotated locations for NP_062706.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK155436, AL731718
      Consensus CDS
      CCDS18782.1
      UniProtKB/TrEMBL
      Q3U1Q3
      Related
      ENSMUSP00000050353.8, ENSMUST00000056977.14
      Conserved Domains (2) summary
      pfam00853
      Location:77198
      Runt; Runt domain
      pfam08504
      Location:328423
      RunxI; Runx inhibition 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_000070.7 Reference GRCm39 C57BL/6J

      Range
      134847956..134905301
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006538506.5XP_006538569.1  runt-related transcription factor 3 isoform X1

      See identical proteins and their annotated locations for XP_006538569.1

      Conserved Domains (2) summary
      pfam00853
      Location:174
      Runt; Runt domain
      pfam08504
      Location:204299
      RunxI; Runx inhibition domain