Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RUNX3 Gene

Aliases for RUNX3 Gene

  • Runt Related Transcription Factor 3 2 3 5
  • Polyomavirus Enhancer-Binding Protein 2 Alpha C Subunit 3 4
  • SL3/AKV Core-Binding Factor Alpha C Subunit 3 4
  • SL3-3 Enhancer Factor 1 Alpha C Subunit 3 4
  • Runt-Related Transcription Factor 3 2 3
  • Core-Binding Factor Subunit Alpha-3 3 4
  • Acute Myeloid Leukemia 2 Protein 3 4
  • Oncogene AML-2 3 4
  • CBF-Alpha-3 3 4
  • CBFA3 3 4
  • AML2 3 4
  • Core-Binding Factor, Runt Domain, Alpha Subunit 3 3
  • Acute Myeloid Leukemia Gene 2 3
  • Transcription Factor AML2 3
  • PEBP2 Alpha C 3
  • PEBP2-Alpha C 4
  • PEA2 Alpha C 3
  • PEA2-Alpha C 4
  • PEBP2aC 3
  • PEBP2A3 4

External Ids for RUNX3 Gene

Previous HGNC Symbols for RUNX3 Gene

  • CBFA3

Previous GeneCards Identifiers for RUNX3 Gene

  • GC01M024749
  • GC01M024294
  • GC01M024205
  • GC01M024577
  • GC01M024971
  • GC01M025098
  • GC01M025226
  • GC01M023479

Summaries for RUNX3 Gene

Entrez Gene Summary for RUNX3 Gene

  • 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]

GeneCards Summary for RUNX3 Gene

RUNX3 (Runt Related Transcription Factor 3) is a Protein Coding gene. Diseases associated with RUNX3 include Gastric Cancer and Testicular Yolk Sac Tumor. Among its related pathways are Notch signaling pathway (KEGG) and Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and RNA polymerase II regulatory region sequence-specific DNA binding. An important paralog of this gene is RUNX2.

UniProtKB/Swiss-Prot for RUNX3 Gene

  • CBF binds to the core site, 5-PYGPYGGT-3, of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, lck, IL-3 and GM-CSF promoters. In association with ZFHX3, upregulates CDKN1A promoter activity following TGF-beta stimulation (PubMed:20599712).

Gene Wiki entry for RUNX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RUNX3 Gene

Genomics for RUNX3 Gene

Regulatory Elements for RUNX3 Gene

Enhancers for RUNX3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G024908 2.1 FANTOM5 Ensembl ENCODE dbSUPER 38.9 +45.4 45407 22.8 CREB3L1 MLX AGO1 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 ZNF263 RUNX3 SYF2 PNRC2 ENSG00000261349 RCAN3 ENSG00000231953 RNU6-1208P RSRP1 ENSG00000225643 SRRM1
GH01G025020 1.9 FANTOM5 Ensembl ENCODE dbSUPER 21.8 -57.5 -57536 4.9 HDGF PKNOX1 ZFP64 WRNIP1 SIN3A YBX1 GLIS2 ELK1 ZNF143 ZNF207 RUNX3 LOC105376878 RSRP1 SYF2 SRRM1 MIR4425 GC01M024955
GH01G025030 2 FANTOM5 Ensembl ENCODE dbSUPER 17.3 -68.4 -68401 6.2 HDGF PKNOX1 CREB3L1 WRNIP1 FEZF1 YBX1 GLI4 GATA2 ZNF207 FOS RUNX3 SYF2 LOC105376878 ENSG00000261349 RSRP1 SDHDP6 MAN1C1 LOC105376879 MIR4425
GH01G025028 1.8 FANTOM5 Ensembl ENCODE dbSUPER 16.5 -64.0 -63979 0.9 HDGF PKNOX1 ARNT CREB3L1 YBX1 TCF12 GATA2 ELK1 JUNB TBX21 RUNX3 LOC105376878 MAN1C1 RSRP1 SYF2 MIR4425 LOC105376879
GH01G025098 1.1 Ensembl ENCODE 12.1 -134.7 -134734 2.4 ELF3 HDGF PKNOX1 FOXA2 YY1 RELB IKZF2 EGR2 SMARCA5 CEBPB RUNX3 LOC105376878 SELENON ENSG00000233755 LOC105376879
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RUNX3 on UCSC Golden Path with GeneCards custom track

Genomic Location for RUNX3 Gene

Chromosome:
1
Start:
24,899,511 bp from pter
End:
24,965,157 bp from pter
Size:
65,647 bases
Orientation:
Minus strand

Genomic View for RUNX3 Gene

Genes around RUNX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RUNX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RUNX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RUNX3 Gene

Proteins for RUNX3 Gene

  • Protein details for RUNX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13761-RUNX3_HUMAN
    Recommended name:
    Runt-related transcription factor 3
    Protein Accession:
    Q13761
    Secondary Accessions:
    • B1AJV5
    • Q12969
    • Q13760

    Protein attributes for RUNX3 Gene

    Size:
    415 amino acids
    Molecular mass:
    44356 Da
    Quaternary structure:
    • Heterodimer of an alpha and a beta subunit. The alpha subunit binds DNA as a monomer and through the Runt domain. DNA-binding is increased by heterodimerization. Interacts with TLE1 and SUV39H1. The tyrosine phosphorylated form (via runt domain) interacts with SRC (via protein kinase domain). Interacts with FYN and LCK. Interacts with FOXP3. Interacts with ZFHX3.

    Alternative splice isoforms for RUNX3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RUNX3 Gene

Post-translational modifications for RUNX3 Gene

  • Phosphorylated on tyrosine residues by SRC. Phosphorylated by LCK and FYN.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RUNX3 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for RUNX3 (AML2)

No data available for DME Specific Peptides for RUNX3 Gene

Domains & Families for RUNX3 Gene

Graphical View of Domain Structure for InterPro Entry

Q13761

UniProtKB/Swiss-Prot:

RUNX3_HUMAN :
  • A proline/serine/threonine rich region at the C-terminus is necessary for transcriptional activation of target genes.
Domain:
  • A proline/serine/threonine rich region at the C-terminus is necessary for transcriptional activation of target genes.
genes like me logo Genes that share domains with RUNX3: view

No data available for Gene Families for RUNX3 Gene

Function for RUNX3 Gene

Molecular function for RUNX3 Gene

GENATLAS Biochemistry:
Drosophila Runt pair rule-related transcription factor 3,expressed in various lymphoid and myeloid cells,involved in hematopoiesis and osteogenesis
UniProtKB/Swiss-Prot Function:
CBF binds to the core site, 5-PYGPYGGT-3, of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, lck, IL-3 and GM-CSF promoters. In association with ZFHX3, upregulates CDKN1A promoter activity following TGF-beta stimulation (PubMed:20599712).

Gene Ontology (GO) - Molecular Function for RUNX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding ISS --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA,ISS --
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 7607690
GO:0005515 protein binding IPI 9751710
genes like me logo Genes that share ontologies with RUNX3: view
genes like me logo Genes that share phenotypes with RUNX3: view

Animal Models for RUNX3 Gene

MGI Knock Outs for RUNX3:

Animal Model Products

CRISPR Products

miRNA for RUNX3 Gene

miRTarBase miRNAs that target RUNX3

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RUNX3 Gene

Localization for RUNX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RUNX3 Gene

Nucleus. Cytoplasm. Note=The tyrosine phosphorylated form localizes to the cytoplasm. Translocates from the cytoplasm to the nucleus following TGF-beta stimulation. {ECO:0000269 PubMed:20599712}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RUNX3 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 2
golgi apparatus 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for RUNX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISS --
GO:0005634 nucleus IEA,IDA 20100835
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IDA 20100835
genes like me logo Genes that share ontologies with RUNX3: view

Pathways & Interactions for RUNX3 Gene

genes like me logo Genes that share pathways with RUNX3: view

Pathways by source for RUNX3 Gene

SIGNOR curated interactions for RUNX3 Gene

Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for RUNX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0001503 ossification IBA --
GO:0002062 chondrocyte differentiation IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated NAS 7622058
genes like me logo Genes that share ontologies with RUNX3: view

Drugs & Compounds for RUNX3 Gene

(1) Drugs for RUNX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(4) Additional Compounds for RUNX3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RUNX3: view

Transcripts for RUNX3 Gene

Unigene Clusters for RUNX3 Gene

Runt-related transcription factor 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RUNX3 Gene

No ASD Table

Relevant External Links for RUNX3 Gene

GeneLoc Exon Structure for
RUNX3
ECgene alternative splicing isoforms for
RUNX3

Expression for RUNX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RUNX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RUNX3 Gene

This gene is overexpressed in Whole Blood (x16.1) and Spleen (x4.8).

Protein differential expression in normal tissues from HIPED for RUNX3 Gene

This gene is overexpressed in NK cells (28.2), Peripheral blood mononuclear cells (15.7), CD8 Tcells (10.1), and CD4 Tcells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RUNX3 Gene



Protein tissue co-expression partners for RUNX3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RUNX3 Gene:

RUNX3

SOURCE GeneReport for Unigene cluster for RUNX3 Gene:

Hs.170019

mRNA Expression by UniProt/SwissProt for RUNX3 Gene:

Q13761-RUNX3_HUMAN
Tissue specificity: Expressed in gastric cancer tissues (at protein level).

Evidence on tissue expression from TISSUES for RUNX3 Gene

  • Skin(4.3)
  • Blood(2.8)
  • Intestine(2.6)
  • Lymph node(2.5)
  • Stomach(2.5)
  • Bone marrow(2.4)
  • Spleen(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with RUNX3: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RUNX3 Gene

Orthologs for RUNX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RUNX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RUNX3 34 35
  • 99.38 (n)
dog
(Canis familiaris)
Mammalia LOC487366 34
  • 92.12 (n)
RUNX3 35
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RUNX3 34 35
  • 91.58 (n)
mouse
(Mus musculus)
Mammalia Runx3 34 16 35
  • 89.18 (n)
rat
(Rattus norvegicus)
Mammalia Runx3 34
  • 88.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 88 (a)
ManyToMany
-- 35
  • 40 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia RUNX3 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves RUNX3 34 35
  • 80.56 (n)
lizard
(Anolis carolinensis)
Reptilia RUNX3 35
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia runx3 34
  • 72.55 (n)
zebrafish
(Danio rerio)
Actinopterygii runx3 34 35
  • 68.02 (n)
-- 34
fruit fly
(Drosophila melanogaster)
Insecta CG1379 36
  • 73 (a)
CG15455 36
  • 67 (a)
run 36 35
  • 67 (a)
lz 36 35
  • 63 (a)
RunxA 35
  • 18 (a)
ManyToMany
RunxB 35
  • 17 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea rnt-1 35
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 65 (a)
OneToMany
Species where no ortholog for RUNX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RUNX3 Gene

ENSEMBL:
Gene Tree for RUNX3 (if available)
TreeFam:
Gene Tree for RUNX3 (if available)

Paralogs for RUNX3 Gene

Paralogs for RUNX3 Gene

(6) SIMAP similar genes for RUNX3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RUNX3: view

Variants for RUNX3 Gene

Sequence variations from dbSNP and Humsavar for RUNX3 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000081063 -- 24,956,278(+) TTCTT(C/T)CTCTG intron-variant
rs1000100250 -- 24,918,414(+) GTCAT(C/G)AAGAT intron-variant
rs1000174179 -- 24,902,864(+) GCTGG(C/T)TGGAG intron-variant
rs1000295993 -- 24,945,474(+) ATAGC(C/T)GCTTC intron-variant, nc-transcript-variant
rs1000302882 -- 24,940,645(+) TCTCA(G/T)CTACT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RUNX3 Gene

Variant ID Type Subtype PubMed ID
nsv1077252 CNV deletion 25765185
nsv1136070 CNV deletion 24896259
nsv508581 CNV deletion 20534489

Variation tolerance for RUNX3 Gene

Residual Variation Intolerance Score: 26.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.57; 12.28% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RUNX3 Gene

Human Gene Mutation Database (HGMD)
RUNX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RUNX3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RUNX3 Gene

Disorders for RUNX3 Gene

MalaCards: The human disease database

(11) MalaCards diseases for RUNX3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
gastric cancer
  • stomach cancer
testicular yolk sac tumor
  • yolk sac tumor
esophagus squamous cell carcinoma
  • esophageal squamous cell carcinoma
salivary gland adenoid cystic carcinoma
  • adenoid cystic cancer
inflammatory bowel disease 7
  • ibd7
- elite association - COSMIC cancer census association via MalaCards
Search RUNX3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RUNX3

Genetic Association Database (GAD)
RUNX3
Human Genome Epidemiology (HuGE) Navigator
RUNX3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RUNX3
genes like me logo Genes that share disorders with RUNX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RUNX3 Gene

Publications for RUNX3 Gene

  1. Src kinase phosphorylates RUNX3 at tyrosine residues and localizes the protein in the cytoplasm. (PMID: 20100835) Goh Y.M. … Bae S.C. (J. Biol. Chem. 2010) 3 4 22 64
  2. Chromatin immunoprecipitation and association study revealed a possible role of Runt-related transcription factor 3 in the ulcerative colitis of Chinese population. (PMID: 20392673) Guo C. … Ding J. (Clin. Immunol. 2010) 3 22 46 64
  3. [The relationship between RUNX3 gene mutation and keloid]. (PMID: 18717361) Zhang G. … Yu Q. (Zhonghua Zheng Xing Wai Ke Za Zhi 2008) 3 22 46 64
  4. Genetic variants in RUNX3 and risk of bladder cancer: a haplotype-based analysis. (PMID: 18684727) Zhang Z. … Zhang Z. (Carcinogenesis 2008) 3 22 46 64
  5. AML1, AML2, and AML3, the human members of the runt domain gene- family: cDNA structure, expression, and chromosomal localization. (PMID: 7835892) Levanon D. … Groner Y. (Genomics 1994) 2 3 4 64

Products for RUNX3 Gene

Sources for RUNX3 Gene

Content
Loading form....