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

Gene ID: 864, updated on 10-Oct-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
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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 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

  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

  2. XM_054339350.1XP_054195325.1  runt-related transcription factor 3 isoform X2