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    RUNX3 RUNX family transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 864, updated on 9-Dec-2024

    Summary

    Official Symbol
    RUNX3provided by HGNC
    Official Full Name
    RUNX family transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:10473
    See related
    Ensembl:ENSG00000020633 MIM:600210; AllianceGenome:HGNC:10473
    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
    AML2; CBFA3; PEBP2aC
    Summary
    This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
    Expression
    Biased expression in bone marrow (RPKM 19.5), spleen (RPKM 16.7) and 12 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RUNX3 in Genome Data Viewer
    Location:
    1p36.11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (24899511..24965138, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24735232..24800883, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (25226002..25291501, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chloride intracellular channel 4 Neighboring gene RNA, U6 small nuclear 1208, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25173940-25174664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 441 Neighboring gene uncharacterized LOC105376876 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:25192786-25193985 Neighboring gene MPRA-validated peak122 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 411 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25240971-25241486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25254973-25255707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25255708-25256441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25257881-25258470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25264973-25265472 Neighboring gene microRNA 6731 Neighboring gene RUNX3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25276177-25276700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25276701-25277226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 446 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:25281264-25282463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25310883-25311384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25316159-25316660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25345941-25346837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25347096-25347624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25347625-25348151 Neighboring gene enhancer 2 sub-fragment of super enhancer upstream of RUNX3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25351623-25352296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25353935-25354474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25354475-25355012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25355013-25355552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 441 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25372889-25373429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25373430-25373969 Neighboring gene microRNA 4425 Neighboring gene long intergenic non-protein coding RNA 2793

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
    EBI GWAS Catalog
    Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility.
    EBI GWAS Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of runt-related transcription factor 3 (RUNX3) in human B 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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ34510, MGC16070

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in chondrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in hemopoiesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of CD4-positive, alpha-beta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of epithelial cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ossification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in peripheral nervous system neuron development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of CD8-positive, alpha-beta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of core-binding factor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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
    acute myeloid leukemia gene 2
    core-binding factor subunit alpha-3
    core-binding factor, runt domain, alpha subunit 3
    oncogene AML-2
    polyomavirus enhancer-binding protein 2 alpha C subunit
    runt related transcription factor 3
    transcription factor AML2

    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_001031680.2NP_001026850.1  runt-related transcription factor 3 isoform 1

      See identical proteins and their annotated locations for NP_001026850.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as p46, represents the longest transcript and encodes the longer isoform (1). Variants 1 and 3 encode the same protein.
      Source sequence(s)
      AI375031, AL023096, BC013362, DA935726
      Consensus CDS
      CCDS30633.1
      UniProtKB/TrEMBL
      B4DVE5
      Related
      ENSP00000382800.1, ENST00000399916.5
      Conserved Domains (3) summary
      pfam00853
      Location:76197
      Runt; Runt domain
      pfam08504
      Location:330429
      RunxI; Runx inhibition domain
      cl26464
      Location:191325
      Atrophin-1; Atrophin-1 family
    2. NM_001320672.1NP_001307601.1  runt-related transcription factor 3 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same protein.
      Source sequence(s)
      AL023096, AL445471, BC013362
      Consensus CDS
      CCDS30633.1
      UniProtKB/TrEMBL
      B4DVE5
      Related
      ENSP00000343477.3, ENST00000338888.4
      Conserved Domains (3) summary
      pfam00853
      Location:76197
      Runt; Runt domain
      pfam08504
      Location:330429
      RunxI; Runx inhibition domain
      cl26464
      Location:191325
      Atrophin-1; Atrophin-1 family
    3. NM_004350.3NP_004341.1  runt-related transcription factor 3 isoform 2

      See identical proteins and their annotated locations for NP_004341.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as p44, contains a distinct 5' UTR and uses an alternate translation initiation site, compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus when compared to isoform 1.
      Source sequence(s)
      AI375031, AJ001432, AL023096, Z35278
      Consensus CDS
      CCDS257.1
      UniProtKB/Swiss-Prot
      B1AJV5, Q12969, Q13760, Q13761
      UniProtKB/TrEMBL
      B4DVE5
      Related
      ENSP00000308051.6, ENST00000308873.11
      Conserved Domains (2) summary
      pfam00853
      Location:62183
      Runt; Runt domain
      pfam08504
      Location:316415
      RunxI; Runx inhibition domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      24899511..24965138 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005246024.5XP_005246081.1  runt-related transcription factor 3 isoform X1

      See identical proteins and their annotated locations for XP_005246081.1

      UniProtKB/TrEMBL
      B4DVE5
      Conserved Domains (3) summary
      pfam00853
      Location:76197
      Runt; Runt domain
      pfam08504
      Location:330429
      RunxI; Runx inhibition domain
      cl26464
      Location:191325
      Atrophin-1; Atrophin-1 family
    2. XM_047433131.1XP_047289087.1  runt-related transcription factor 3 isoform X1

      UniProtKB/TrEMBL
      B4DVE5
    3. XM_011542351.2XP_011540653.1  runt-related transcription factor 3 isoform X2

      UniProtKB/TrEMBL
      B4DVE5
      Conserved Domains (2) summary
      pfam00853
      Location:76196
      Runt; Runt domain
      pfam08504
      Location:277376
      RunxI; Runx inhibition domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      24735232..24800883 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339349.1XP_054195324.1  runt-related transcription factor 3 isoform X1

      UniProtKB/TrEMBL
      B4DVE5
    2. XM_054339350.1XP_054195325.1  runt-related transcription factor 3 isoform X2

      UniProtKB/TrEMBL
      B4DVE5