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    RUNX2 runt related transcription factor 2 [ Homo sapiens (human) ]

    Gene ID: 860, updated on 14-Jun-2016
    Official Symbol
    RUNX2provided by HGNC
    Official Full Name
    runt related transcription factor 2provided by HGNC
    Primary source
    HGNC:HGNC:10472
    See related
    Ensembl:ENSG00000124813 HPRD:02566; MIM:600211; Vega:OTTHUMG00000014774
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CCD; AML3; CCD1; CLCD; OSF2; CBFA1; OSF-2; PEA2aA; PEBP2aA; CBF-alpha-1
    Summary
    This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. 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. Mutations in this gene have been associated with the bone development disorder cleidocranial dysplasia (CCD). Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    6p21
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (45328142..45664032)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45296054..45518819)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene SPT3 homolog, SAGA and STAGA complex component Neighboring gene poly(rC) binding protein 2 pseudogene Neighboring gene microRNA 586 Neighboring gene uncharacterized LOC105375077 Neighboring gene uncharacterized LOC107986519 Neighboring gene uncharacterized LOC105375078 Neighboring gene chloride intracellular channel 5

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Cleidocranial dysostosis
    MedGen: C0008928 OMIM: 119600 GeneReviews: Cleidocranial Dysplasia
    Compare labs
    Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly
    MedGen: C1834969 OMIM: 156510 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Genome-wide association study of periodontal pathogen colonization.
    NHGRI GWA Catalog
    Many sequence variants affecting diversity of adult human height.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env In human osteoblast (hOB) cell lines, HIV-1 Gag and gp120 reduce RUNX-2 and PPAR-gamma mRNA expression and activity PubMed
    Nef nef HIV-1 Nef downregulates the expression of RUNX2 protein in human mesenchymal stem cells PubMed
    Pr55(Gag) gag In human osteoblast (hOB) cell lines, HIV-1 Gag and gp120 reduce RUNX-2 and PPAR-gamma mRNA expression and activity PubMed
    Tat tat HIV-1 Tat downregulates the expression of RUNX2 protein in human mesenchymal stem cells PubMed
    Vif vif The binding of HIV-1 Vif to CBF-beta is mutually exclusive of endogenous RUNX transcriptional factors in cells. Vif inhibits transcription of a RUNX1 reporter gene by competition with CBF-beta PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC120022, MGC120023

    Gene Ontology Provided by GOA

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

    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.

    Genomic

    1. NG_008020.1 RefSeqGene

      Range
      5001..227766
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001015051.3NP_001015051.3  runt-related transcription factor 2 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (b, also known as OSF2/CBF1b) is shorter, compared to isoform a.
      Source sequence(s)
      AL096865, AL161907, AL358135
      Consensus CDS
      CCDS43468.2
      UniProtKB/Swiss-Prot
      Q13950
      Related
      ENSP00000360486, ENST00000371432
      Conserved Domains (2) summary
      pfam00853
      Location:99233
      Runt; Runt domain
      pfam08504
      Location:405499
      RunxI; Runx inhibition domain
    2. NM_001024630.3NP_001019801.3  runt-related transcription factor 2 isoform a

      See identical proteins and their annotated locations for NP_001019801.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a, also known as OSF2/CBFA1a).
      Source sequence(s)
      AL096865, AL161907, AL358135
      Consensus CDS
      CCDS43467.2
      UniProtKB/Swiss-Prot
      Q13950
      Related
      ENSP00000420707, OTTHUMP00000016533, ENST00000465038, OTTHUMT00000040754
      Conserved Domains (2) summary
      pfam00853
      Location:99233
      Runt; Runt domain
      pfam08504
      Location:427521
      RunxI; Runx inhibition domain
    3. NM_001278478.1NP_001265407.1  runt-related transcription factor 2 isoform d

      See identical proteins and their annotated locations for NP_001265407.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5'-most exon, lacks an in-frame exon in the 3' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct and shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AL161907, BC108919, DR005078
      Consensus CDS
      CCDS64443.1
      UniProtKB/TrEMBL
      A0A0D9SEN7, Q32MY8
      Related
      ENSP00000485863, OTTHUMP00000279213, ENST00000625924, OTTHUMT00000484119
      Conserved Domains (2) summary
      pfam00853
      Location:85219
      Runt; Runt domain
      pfam08504
      Location:391485
      RunxI; Runx inhibition domain

    RNA

    1. NR_103532.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5'-terminal exon, lacks several exons, and contains an alternate 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region and does not encode a supported protein.
      Source sequence(s)
      AL096865, AW469546, BX108677
      Related
      ENST00000483243
    2. NR_103533.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several exons, and contains an alternate 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region and does not encode a supported protein.
      Source sequence(s)
      AL096865, AW469546, BX108677

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

      Range
      45328142..45664032
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011391.1XP_016866880.1  

    2. XM_011514960.2XP_011513262.1  

      Conserved Domains (1) summary
      pfam00853
      Location:167301
      Runt; Runt domain
    3. XM_011514963.2XP_011513265.1  

      Conserved Domains (1) summary
      pfam00853
      Location:167300
      Runt; Runt domain
    4. XM_011514961.2XP_011513263.1  

      Conserved Domains (2) summary
      pfam00853
      Location:167301
      Runt; Runt domain
      pfam08504
      Location:495589
      RunxI; Runx inhibition domain
    5. XM_011514964.2XP_011513266.1  

      Conserved Domains (1) summary
      pfam00853
      Location:167301
      Runt; Runt domain
    6. XM_011514962.2XP_011513264.1  

      Conserved Domains (2) summary
      pfam00853
      Location:167301
      Runt; Runt domain
      pfam08504
      Location:473567
      RunxI; Runx inhibition domain
    7. XM_017011393.1XP_016866882.1  

    8. XM_011514965.2XP_011513267.1  

      Conserved Domains (1) summary
      pfam00853
      Location:167301
      Runt; Runt domain
    9. XM_017011394.1XP_016866883.1  

    10. XM_017011395.1XP_016866884.1  

    11. XM_017011392.1XP_016866881.1  

      Related
      ENSP00000458178, OTTHUMP00000257615, ENST00000576263, OTTHUMT00000438832
    12. XM_006715232.1XP_006715295.1  

      See identical proteins and their annotated locations for XP_006715295.1

      Conserved Domains (2) summary
      pfam00853
      Location:85218
      Runt; Runt domain
      pfam08504
      Location:355449
      RunxI; Runx inhibition domain
    13. XM_017011396.1XP_016866885.1  

      Related
      ENSP00000460188, OTTHUMP00000257616, ENST00000478660, OTTHUMT00000438833
    14. XM_011514966.2XP_011513268.1  

      Conserved Domains (1) summary
      pfam00853
      Location:177
      Runt; Runt domain

    RNA

    1. XR_926323.2 RNA Sequence

    2. XR_001743701.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      45298649..45521390
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_004348.3: Suppressed sequence

      Description
      NM_004348.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.