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    Runx2 runt related transcription factor 2 [ Mus musculus (house mouse) ]

    Gene ID: 12393, updated on 16-May-2017
    Official Symbol
    Runx2provided by MGI
    Official Full Name
    runt related transcription factor 2provided by MGI
    Primary source
    MGI:MGI:99829
    See related
    Ensembl:ENSMUSG00000039153 Vega:OTTMUSG00000033514
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cbf; LS3; AML3; Osf2; Cbfa1; Cbfa-1; PEBP2aA; Pebp2a1; Pebpa2a
    Summary
    This gene encodes a member of the runt domain-containing family of transcription factors. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Sep 2015]
    Orthologs
    Location:
    17 B3; 17 21.33 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 17 NC_000083.6 (44495986..44814831, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (44740950..44951746, complement)

    Chromosome 17 - NC_000083.6Genomic Context describing neighboring genes Neighboring gene predicted gene, 34917 Neighboring gene chloride intracellular channel 5 Neighboring gene runt related transcription factor 2, opposite strand 3 Neighboring gene RIKEN cDNA 4930564C03 gene Neighboring gene suppressor of Ty 3 Neighboring gene predicted gene, 35097

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    bHLH transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    repressing transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    transcription regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    T cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell maturation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cell maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to BMP stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chondrocyte development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chondrocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    chondrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic cranial skeleton morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    embryonic forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endochondral ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of smoothened signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    odontogenesis of dentin-containing tooth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    osteoblast development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    osteoblast differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    osteoblast fate commitment IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of chondrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of ossification ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of osteoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of osteoblast differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of fibroblast growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of odontogenesis of dentin-containing tooth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of osteoblast differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    skeletal system morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    transcription factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    runt-related transcription factor 2
    Names
    AKV core binding factor
    CBF-alpha-1
    PEA2-alpha A
    PEBP2 alpha A
    SL3-3 enhancer factor 1 alpha A subunit
    acute myeloid leukemia 3 protein
    core binding factor alpha 1
    osteoblast-specific transcription factor 2
    polyomavirus enhancer-binding protein 2 alpha A subunit
    runt domain, alpha subunit 1

    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_001145920.2NP_001139392.1  runt-related transcription factor 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents use of a proximal promoter. It lacks two alternate exons including the 5' UTR and a portion of the 5' coding region, and initiates translation in an alternate 5' segment, compared to variant 1. The encoded isoform (2, also known as MRIPV) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC165141
      Consensus CDS
      CCDS50116.1
      UniProtKB/TrEMBL
      F8WHN7
      Related
      ENSMUSP00000109202.2, OTTMUSP00000045415, ENSMUST00000113572.8, OTTMUST00000084308
      Conserved Domains (2) summary
      pfam00853
      Location:102223
      Runt; Runt domain
      pfam08504
      Location:423514
      RunxI; Runx inhibition domain
    2. NM_001146038.2NP_001139510.1  runt-related transcription factor 2 isoform 1

      See identical proteins and their annotated locations for NP_001139510.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents use of a distal promoter. It encodes the longest isoform (1, also called MASNS).
      Source sequence(s)
      AC165141, AF010284, AF020681
      Consensus CDS
      CCDS37624.2
      UniProtKB/Swiss-Prot
      Q08775
      UniProtKB/TrEMBL
      Q9Z2T9
      Related
      ENSMUSP00000109201.3, ENSMUST00000113571.9
      Conserved Domains (2) summary
      pfam00853
      Location:116237
      Runt; Runt domain
      pfam08504
      Location:437528
      RunxI; Runx inhibition domain
    3. NM_001271627.1NP_001258556.1  runt-related transcription factor 2 isoform 1

      See identical proteins and their annotated locations for NP_001258556.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents use of a distal promoter. It has an additional segment in 5' UTR and encodes the same isoform 1, compared to variant 1. This variant is reported in PMID: 9238031.
      Source sequence(s)
      AC165141, AL672242
      Consensus CDS
      CCDS37624.2
      UniProtKB/Swiss-Prot
      Q08775
      Related
      ENSMUSP00000124918.1, OTTMUSP00000045416, ENSMUST00000159943.7, OTTMUST00000084309
      Conserved Domains (2) summary
      pfam00853
      Location:116237
      Runt; Runt domain
      pfam08504
      Location:437528
      RunxI; Runx inhibition domain
    4. NM_001271630.1NP_001258559.1  runt-related transcription factor 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) represents use of a proximal promoter. It lacks two alternate exons including the 5' UTR and a portion of the 5' coding region, initiates translation in an alternate 5' segment, and lacks an internal in-frame coding exon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC165141
      Conserved Domains (2) summary
      pfam00853
      Location:102222
      Runt; Runt domain
      pfam08504
      Location:365456
      RunxI; Runx inhibition domain
    5. NM_001271631.1NP_001258560.1  runt-related transcription factor 2 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) represents use of a proximal promoter. It lacks two alternate exons including the 5' UTR and a portion of the 5' coding region, initiates translation in an alternate 5' segment, and lacks two internal in-frame coding exons, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC165141, AK089291, AK158925
      Consensus CDS
      CCDS70815.1
      UniProtKB/TrEMBL
      E0CZ12
      Related
      ENSMUSP00000123707.1, OTTMUSP00000045420, ENSMUST00000162878.7, OTTMUST00000084315
      Conserved Domains (2) summary
      pfam00853
      Location:102186
      Runt; Runt domain
      pfam08504
      Location:330421
      RunxI; Runx inhibition domain
    6. NM_009820.5NP_033950.2  runt-related transcription factor 2 isoform 1

      See identical proteins and their annotated locations for NP_033950.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents use of a distal promoter. It lacks a segment in 5' UTR and encodes the same isoform 1, compared to variant 1.
      Source sequence(s)
      AC165141, AF010284
      Consensus CDS
      CCDS37624.2
      UniProtKB/Swiss-Prot
      Q08775
      Conserved Domains (2) summary
      pfam00853
      Location:116237
      Runt; Runt domain
      pfam08504
      Location:437528
      RunxI; Runx inhibition domain

    RNA

    1. NR_073392.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) represents use of a distal promoter. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC165141, DQ458792
    2. NR_073425.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) represents use of a proximal promoter. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK158925
      Related
      ENSMUST00000162816.7, OTTMUST00000084314

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000083.6 Reference GRCm38.p4 C57BL/6J

      Range
      44495986..44814831 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006523542.2XP_006523605.1  runt-related transcription factor 2 isoform X3

      Conserved Domains (1) summary
      pfam00853
      Location:184305
      Runt; Runt domain
    2. XM_006523541.2XP_006523604.1  runt-related transcription factor 2 isoform X2

      Conserved Domains (1) summary
      pfam00853
      Location:195316
      Runt; Runt domain
    3. XM_006523546.2XP_006523609.1  runt-related transcription factor 2 isoform X7

      Conserved Domains (1) summary
      pfam00853
      Location:220340
      Runt; Runt domain
    4. XM_006523540.2XP_006523603.1  runt-related transcription factor 2 isoform X1

      Conserved Domains (1) summary
      pfam00853
      Location:220341
      Runt; Runt domain
    5. XM_006523545.2XP_006523608.1  runt-related transcription factor 2 isoform X6

      See identical proteins and their annotated locations for XP_006523608.1

      UniProtKB/Swiss-Prot
      Q08775
      Related
      ENSMUSP00000123743.1, OTTMUSP00000045414, ENSMUST00000160673.7, OTTMUST00000084307
      Conserved Domains (2) summary
      pfam00853
      Location:184305
      Runt; Runt domain
      pfam08504
      Location:505596
      RunxI; Runx inhibition domain
    6. XM_006523544.2XP_006523607.1  runt-related transcription factor 2 isoform X5

      See identical proteins and their annotated locations for XP_006523607.1

      UniProtKB/Swiss-Prot
      Q08775
      Conserved Domains (2) summary
      pfam00853
      Location:195316
      Runt; Runt domain
      pfam08504
      Location:516607
      RunxI; Runx inhibition domain
    7. XM_006523548.2XP_006523611.1  runt-related transcription factor 2 isoform X9

      Conserved Domains (2) summary
      pfam00853
      Location:220340
      Runt; Runt domain
      pfam08504
      Location:461552
      RunxI; Runx inhibition domain
    8. XM_006523547.2XP_006523610.1  runt-related transcription factor 2 isoform X8

      Conserved Domains (2) summary
      pfam00853
      Location:220340
      Runt; Runt domain
      pfam08504
      Location:483574
      RunxI; Runx inhibition domain
    9. XM_006523543.2XP_006523606.1  runt-related transcription factor 2 isoform X4

      Related
      ENSMUSP00000124374.1, OTTMUSP00000045422, ENSMUST00000162629.7, OTTMUST00000084317
      Conserved Domains (2) summary
      pfam00853
      Location:220341
      Runt; Runt domain
      pfam08504
      Location:519610
      RunxI; Runx inhibition domain

    RNA

    1. XR_385274.2 RNA Sequence

    2. XR_385272.3 RNA Sequence

    3. XR_385271.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001271633.1: Suppressed sequence

      Description
      NM_001271633.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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