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RUNX3 runt related transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 864, updated on 11-Nov-2018

Summary

Official Symbol
RUNX3provided by HGNC
Official Full Name
runt related transcription factor 3provided by HGNC
Primary source
HGNC:HGNC:10473
See related
Ensembl:ENSG00000020633 MIM:600210; Vega:OTTHUMG00000003316
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

Genomic context

See RUNX3 in Genome Data Viewer
Location:
1p36.11
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (24899511..24965158, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (25226002..25291648, 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 uncharacterized LOC105376876 Neighboring gene uncharacterized LOC107984932 Neighboring gene uncharacterized LOC105376878 Neighboring gene microRNA 6731 Neighboring gene enhancer 2 sub-fragment of super enhancer upstream of RUNX3 Neighboring gene uncharacterized LOC105376879 Neighboring gene microRNA 4425

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

  • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
    Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
  • TGF-beta Receptor Signaling, organism-specific biosystem (from WikiPathways)
    TGF-beta Receptor Signaling, organism-specific biosystemThe Transforming growth factor beta (TGFβ) signaling pathway is involved in many cellular processes in both the adult organism and the developing embryo including cell growth, cell differentiat...
  • Th1 and Th2 cell differentiation, organism-specific biosystem (from KEGG)
    Th1 and Th2 cell differentiation, organism-specific biosystemImmunity to different classes of microorganisms is orchestrated by separate lineages of effector T helper (TH)-cells, which differentiate from naive CD4+ precursor cells in response to cues provided ...
  • Th1 and Th2 cell differentiation, conserved biosystem (from KEGG)
    Th1 and Th2 cell differentiation, conserved biosystemImmunity to different classes of microorganisms is orchestrated by separate lineages of effector T helper (TH)-cells, which differentiate from naive CD4+ precursor cells in response to cues provided ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34510, MGC16070

Gene Ontology Provided by GOA

Process Evidence Code Pubs
chondrocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hemopoiesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of CD4-positive, alpha-beta T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cell cycle ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peripheral nervous system neuron development TAS
Traceable Author Statement
more info
PubMed 
positive regulation of CD8-positive, alpha-beta T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
response to transforming growth factor beta IDA
Inferred from Direct Assay
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
core-binding factor complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nuclear chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
transcription factor AML2

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    Q13761
    UniProtKB/TrEMBL
    A0A024RAH4
    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/Swiss-Prot
    Q13761
    UniProtKB/TrEMBL
    A0A024RAH4
    Related
    ENSP00000343477.3, OTTHUMP00000003371, ENST00000338888.3, OTTHUMT00000009285
    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_004350.2NP_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
    Q13761
    Related
    ENSP00000308051.6, OTTHUMP00000003370, ENST00000308873.10, OTTHUMT00000009284
    Conserved Domains (2) summary
    pfam00853
    Location:62183
    Runt; Runt domain
    pfam08504
    Location:316415
    RunxI; Runx inhibition domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    24899511..24965158 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246024.4XP_005246081.1  runt-related transcription factor 3 isoform X1

    See identical proteins and their annotated locations for XP_005246081.1

    UniProtKB/Swiss-Prot
    Q13761
    UniProtKB/TrEMBL
    A0A024RAH4
    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_011542351.1XP_011540653.1  runt-related transcription factor 3 isoform X2

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