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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

RUNX3 Gene

protein-coding GIFtS: 67
GCID: GC01M025226

runt-related transcription factor 3

(Previous symbol: CBFA3)

Explore 61 diseases affiliated with
RUNX3 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Runt-Related Transcription Factor 3¹ ²		PEBP2-Alpha C² ³
AML2¹ ² ³ ⁵		SL3-3 Enhancer Factor 1 Alpha C Subunit² ³
CBFA3¹ ² ³ ⁵		SL3/AKV Core-Binding Factor Alpha C Subunit² ³
PEBP2A3¹ ³ ⁵		PEBP2aC²
Acute Myeloid Leukemia 2 Protein² ³		Acute Myeloid Leukemia Gene 2²
Core-Binding Factor Subunit Alpha-3² ³		Core-Binding Factor, Runt Domain, Alpha Subunit 3²
Oncogene AML-2² ³		PEA2 Alpha C²
Polyomavirus Enhancer-Binding Protein 2 Alpha C Subunit² ³		PEBP2 Alpha C²
CBF-Alpha-3¹		Transcription Factor AML2²
PEA2-Alpha C² ³

External Ids:	HGNC: 10473¹	Entrez Gene: 864²	Ensembl: ENSG00000020633⁷	OMIM: 600210⁵	UniProtKB: Q13761³

ORGUL members:
	NONCODE:n337779

Export aliases for RUNX3 gene to outside databases

Previous GC identifers: GC01M024749 GC01M024294 GC01M024205 GC01M024577 GC01M024971 GC01M025098 GC01M023479

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for RUNX3:

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.

Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: RUNX3_HUMAN, Q13761

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

Gene Wiki entry for RUNX3

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000001.10 NC_018912.1 NT_004610.19

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the RUNX3 gene promoter:
STAT1 STAT2 p300 STAT1beta STAT3 STAT1alpha
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: RUNX3 promoter sequence

Search SABiosciences Chromatin IP Primers for RUNX3

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RUNX3

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36 Ensembl cytogenetic band: 1p36.11 HGNC cytogenetic band: 1p36

RUNX3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RUNX3 gene location

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01M025226: view genomic region (about GC identifiers)

Start:	25,226,002 bp from pter	End:	25,291,612 bp from pter
Size:	65,611 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RUNX3_HUMAN, Q13761 (See protein sequence)

Recommended Name: Runt-related transcription factor 3

Size: 415 amino acids; 44356 Da

Subunit: 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

Subcellular location: Nucleus. Cytoplasm. Note=The tyrosine phosphorylated form localizes to the cytoplasm

Secondary accessions: B1AJV5 Q12969 Q13760

Alternative splicing: 2 isoforms: Q13761-1 Q13761-2

Explore the universe of human proteins at neXtProt for RUNX3: NX_Q13761

Post-translational modifications:

Phosphorylated on tyrosine residues by SRC. Phosphorylated by LCK and FYN¹

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q13761

RUNX3 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_001026850.1 NP_004341.1

ENSEMBL proteins:

ENSP00000308051 ENSP00000343477 ENSP00000382800 ENSP00000444872

Human Recombinant Protein Products for RUNX3:

	Browse Purified and Recombinant Proteins at EMD Millipore
	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells OriGene Protein Over-expression Lysate: RUNX3 OriGene Custom Protein Services for RUNX3
	GenScript Custom Purified and Recombinant Proteins Services for RUNX3
	Novus Biologicals RUNX3 Proteins Novus Biologicals RUNX3 Lysates
	Browse Sino Biological Recombinant Proteins
	ProSpec Recombinant Protein for RUNX3
	Uscn Proteins for RUNX3

Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000790	nuclear chromatin	ISS	--
GO:0005634	nucleus	IDA	--
GO:0005737	cytoplasm	IDA	--

RUNX3 for ontologies About GeneDecksing

RUNX3 Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of RUNX3
	R&D Systems Antibodies for RUNX3 (RUNX3/CBFA3)
	Cell Signaling Technology (CST) Antibodies for RUNX3 (AML2)
	Browse OriGene Antibodies OriGene Custom Antibody Services for RUNX3
	GenScript Superior Antibodies for RUNX3
	Novus Biologicals RUNX3 Antibodies
	Abcam antibodies for RUNX3
	Uscn Antibodies for RUNX3
	ThermoFisher Antibody for RUNX3

Assay Products for RUNX3:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for RUNX3
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for RUNX3

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

RUNX3 for domains About GeneDecksing

5/6 InterPro domains/families (see all 6):

IPR012346 p53/RUNT-type_TF_DNA-bd

IPR000040 AML1_Runt

IPR008967 p53-like_TF_DNA-bd

IPR016554 TF_Runt-rel_RUNX

IPR013711 RunxI

Graphical View of Domain Structure for InterPro Entry Q13761

ProtoNet protein and cluster: Q13761

2 Blocks protein families:

IPB000040 Acute myeloid leukemia 1 protein signature

IPB013711 Runx inhibition

UniProtKB/Swiss-Prot: RUNX3_HUMAN, Q13761

Domain: A proline/serine/threonine rich region at the C-terminus is necessary for transcriptional activation of target

genes

Similarity: Contains 1 Runt domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: RUNX3_HUMAN, Q13761

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

Genatlas biochemistry entry for RUNX3:

Drosophila Runt pair rule-related transcription factor 3,expressed in various lymphoid and myeloid cells,involved in

hematopoiesis and osteogenesis

Gene Ontology (GO): 5/6 molecular function terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	ISS	--
GO:0000981	sequence-specific DNA binding RNA polymerase II transcription factor activity	ISS	--
GO:0003677	DNA binding	--	--
GO:0003700	sequence-specific DNA binding transcription factor activity	TAS	7607690
GO:0005515	protein binding	IPI	18772112

RUNX3 for ontologies About GeneDecksing

Phenotypes:
1 GenomeRNAi human phenotype for RUNX3:

Increased gamma-H2AX phosphory

15/16 MGI mutant phenotypes (inferred from 6 alleles) (MGI details for Runx3) (see all 16):

adipose tissue	behavior/neurological	cellular	digestive/alimentary	endocrine/exocrine gland
growth/size	hematopoietic system	homeostasis/metabolism	immune system	integument
mortality/aging	muscle	nervous system	no phenotypic analysis	respiratory system

RUNX3 for phenotypes About GeneDecksing

Animal Models:
Mouse knock-out Runx3^tm2Yg for RUNX3

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for RUNX3

miRNA Products:		miRTarBase miRNAs that target RUNX3: hsa-mir-130b (MIRT003316), hsa-mir-532-5p (MIRT000038)

		OriGene 3'-UTR Clone (see all 2): RUNX3 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RUNX3
		8/67 QIAGEN miScript miRNA Assays for microRNAs that regulate RUNX3 (see all 67):
		hsa-miR-520e hsa-miR-106a hsa-miR-519a hsa-miR-93 hsa-miR-637 hsa-miR-130b hsa-miR-520b hsa-miR-20a

		SwitchGear 3'UTR luciferase reporter plasmid: RUNX3 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for RUNX3 (see all 7) OriGene shRNA RFP: RUNX3 OriGene siRNA: RUNX3
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RUNX3
		Sirion Biotech Custom design and validation of potent shRNA sequences against RUNX3

Gene Editing Products:			DNA2.0 Custom Protein Engineering Service for RUNX3
			Sirion Biotech Customized adenovirus for overexpression of RUNX3 Sirion Biotech Customized adenovirus for potent knockdown of RUNX3

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RUNX3 (see all 4) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RUNX3 (see all 3) OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 2): RUNX3 (NM_004350)
		Browse Sino Biological Human cDNA Clones
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for RUNX3
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RUNX3

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for RUNX3
		Search LifeMap BioReagents cell lines for RUNX3
		Sirion Biotech Customized stable knockdown cell line services for RUNX3 Sirion Biotech Customized inducible knockdown cell line services for RUNX3 Sirion Biotech Customized stable overexpressing cell line services for RUNX3 Sirion Biotech Customized inducible overexpressing cell line services for RUNX3

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RUNX3

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways About this table

See pathways by source

Super-pathway

contained gene-specific pathways

TGF-beta/Smad Signaling

TGF-beta/Smad Signaling

1.00

SIDS Susceptibility Pathways

SIDS Susceptibility Pathways

1.00

TGF Beta Signaling Pathway

TGF Beta Signaling Pathway

1.00

TGF-beta Signaling Pathways

TGF-beta Signaling Pathways

1.00

Endochondral Ossification

Endochondral Ossification

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

1 R&D Systems Pathway for RUNX3

TGF-beta Signaling Pathways

1 Cell Signaling Technology (CST) Pathway for RUNX3

TGF-beta/Smad Signaling

3 BioSystems Pathways for RUNX3

	TGF Beta Signaling Pathway
	SIDS Susceptibility Pathways
	Endochondral Ossification

RUNX3 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for RUNX3

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

5/47 Interacting proteins for RUNX3 (Q13761^{1, 2, 3} ENSP00000343477⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 47)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
CTNNB1	P35222¹^,³, ENSP00000344456⁴	EBI-1046821,EBI-491549 I2D: score=1 STRING: ENSP00000344456
TCF7L2	Q9NQB0¹^,³, ENSP00000358404⁴	EBI-1046821,EBI-924724 I2D: score=1 STRING: ENSP00000358404
TLE1	Q04724¹^,³, ENSP00000365682⁴	EBI-1046821,EBI-711424 I2D: score=5 STRING: ENSP00000365682
SMAD3	P84022³, ENSP00000332973⁴	I2D: score=3 STRING: ENSP00000332973
HDAC4	P56524³, ENSP00000264606⁴	I2D: score=2 STRING: ENSP00000264606

About this table

Gene Ontology (GO): 5/13 biological process terms (GO ID links to tree view) (see all 13): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	ISS	--
GO:0006355	regulation of transcription, DNA-dependent	NAS	7622058
GO:0006366	transcription from RNA polymerase II promoter	TAS	7607690
GO:0006468	protein phosphorylation	IDA	--
GO:0006917	induction of apoptosis	ISS	--

RUNX3 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

RUNX3 for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for RUNX3
5 Novoseek chemical compound relationships for RUNX3 gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
5-aza-2'deoxycytidine	76.1	14	15386381 (1), 16328045 (1), 18848767 (1), 17384682 (1) (see all 11)
oligonucleotide	0	1	16367903 (1)
serine	0	1	10419474 (1)
retinoic acid	0	10	10419474 (5), 17270239 (1)
vegf	0	5	17085650 (5)

Search CenterWatch for drugs/clinical trials and news about RUNX3

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for RUNX3 gene (2 alternative transcripts):

NM_001031680.2 NM_004350.2

Unigene Cluster for RUNX3:

Runt-related transcription factor 3

Hs.170019 [show with all ESTs]

Unigene Representative Sequence: NM_001031680

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000308873(uc001bjq.3 uc010oen.2) ENST00000338888(uc009vrl.1)

ENST00000496967 ENST00000479341 ENST00000399916(uc009vrj.3 uc001bjr.3 uc009vrk.3)

ENST00000540420

miRNA Products:		OriGene 3'-UTR Clone (see all 2): RUNX3 Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RUNX3
		8/67 QIAGEN miScript miRNA Assays for microRNAs that regulate RUNX3 (see all 67):
		hsa-miR-520e hsa-miR-106a hsa-miR-519a hsa-miR-93 hsa-miR-637 hsa-miR-130b hsa-miR-520b hsa-miR-20a

		SwitchGear 3'UTR luciferase reporter plasmid: RUNX3 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for RUNX3 (see all 7) OriGene shRNA RFP: RUNX3 OriGene siRNA: RUNX3
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RUNX3
		Sirion Biotech Custom design and validation of potent shRNA sequences against RUNX3

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RUNX3 (see all 4) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RUNX3 (see all 3) OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 2): RUNX3 (NM_004350)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for RUNX3
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RUNX3

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RUNX3 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat RUNX3
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RUNX3
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RUNX3

Additional cDNA sequence:

AF022726.2 AJ001432.1 AK091829.1 AK300056.1 AK301044.1 AK310945.1 BC013362.2 EF491807.1

EF491822.1 X79550.2 Z35278.1

10 DOTS entries:

DT.316245 DT.121417079 DT.95272569 DT.121417078 DT.91761550 DT.99935616 DT.91641553 DT.101962196

DT.121417056 DT.86852679

24/168 AceView cDNA sequences (see all 168):

BX107980 AI633590 AI685772 AW304478 CR591302 AI248006 AI524028 AA312733

W94743 BQ708535 CA432310 AW276069 BC013362 AF022726 AA912790 BQ054373

BF478062 AI075058 AI131365 BI908613 BM705361 BQ054372 AA302999 AI092506

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

RUNX3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CTGAGGTGTG

About this image

RUNX3 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

10/28 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 28)

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Bone

Autopod Epiphyseal End

Chondrocytes

Selective marker (cell-identifying gene)

Bone, Cartilage

Bone

Autopod Growth Plate

Prehypertrophic Chondrocytes

Bone, Cartilage

Bone

Caudal Endochondral Bones

Hypertrophic Chondrocytes

Bone, Cartilage

Bone

Caudal Endochondral Bones

Prehypertrophic Chondrocytes

Bone, Cartilage

Bone, Cartilage

Prehypertrophic Chondrocytes

Bone, Cartilage

Bone

Endochondral Facial Bones

Hypertrophic Chondrocytes

Bone, Cartilage

Bone

Endochondral Facial Bones

Prehypertrophic Chondrocytes

Bone, Cartilage

Bone, Cartilage

Prehypertrophic Chondrocytes

Bone, Cartilage

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 8 LifeMap Cells

Name

Category

PureStem™ progenitor E68 (Embryonic Progenitor Cell)

PureStem™ progenitor T42 (Embryonic Progenitor Cell)

PureStem™ progenitor E44 (Embryonic Progenitor Cell)

PureStem™ progenitor EN2 (Embryonic Progenitor Cell)

PureStem™ progenitor EN27 (Embryonic Progenitor Cell)

PureStem™ progenitor EN7 (Embryonic Progenitor Cell)

PureStem™ progenitor W10 (Embryonic Progenitor Cell)

HyStem+BMP4-induced E15 cells (HyStem+BMP4 inductio...)

Adipose, Bone, Cartilage

See RUNX3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for RUNX3

SOURCE GeneReport for Unigene cluster: Hs.170019

SABiosciences Expression via Pathway-Focused PCR Arrays including RUNX3:

Oncogenes & Tumor Suppressor Genes in human mouse rat

Leukemia in human mouse rat

T Helper Cell Differentiation in human mouse rat

Liver Cancer in human mouse rat

Apoptosis 384HT in human mouse rat

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RUNX3 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat RUNX3
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RUNX3
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RUNX3

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RUNX3

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for RUNX3 gene from 5/19 species (see all 19) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	RUNX3¹	runt-related transcription factor 3	80.81(n) 88.38(a)		769687 XM_001232977.2 XP_001232978.2
lizard (Anolis carolinensis)	Reptilia	RUNX3⁶	--	68(a)	1 ↔ 1	GL343464.1(6005-52673)
zebrafish (Danio rerio)	Actinopterygii	AB043788.1²	--	76.94(n)		58127 AB043788.1
fruit fly (Drosophila melanogaster)	Insecta	CG1379³	transcription factor	73(a) (best of 4)		--
worm (Caenorhabditis elegans)	Secernentea	rnt-1⁶	RuNT related family member (rnt-1)	28(a)	1 → many	I(5776157-5788612)

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

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for RUNX3 gene

RUNX1² RUNX2²

6 SIMAP similar genes for RUNX3 using alignment to 2 protein entries: RUNX3_HUMAN (see all proteins):

AML2 RUNX1/C20orf112 fusion RUNX1 RUNX2 RUNX1/CBFA2T2 fusion C20orf112/RUNX1 fusion

RUNX3 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
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SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs7514332^1,2	C,F,A,H	--	25225675(+)	`CTCCCG/CAAATG`	2	--	ds500¹		15		NS EA WA NA CSA	1202
rs115854288^1,2		--	25225680(+)	`GAAATG/CTGAAT`	2	--	ds500¹		1		WA	118
rs190960244^1,2		--	25225777(+)	`GAAGAC/TCTATT`	2	--	ds500¹		0	--	--	--	--
rs182109671^1,2		--	25225856(+)	`TCTGCA/GGCCAT`	2	--	ds500¹		0	--	--	--	--
rs187600926^1,2	C	--	25225929(+)	`GGCAAA/CAGCAG`	2	--	ds500¹		0	--	--	--	--
rs144915186^1,2		--	25225933(+)	`ACAGC-/AGGAGGTC`	2	--	ds500¹		0	--	--	--	--
rs145901854^1,2		--	25225953(+)	`TCTCCC/TCCACC`	2	--	ds500¹		0	--	--	--	--
rs192833531^1,2		--	25225990(+)	`GAAACC/TGGGCA`	2	--	ds500¹		0	--	--	--	--
rs138356545^1,2		--	25226078(+)	`CAGAAA/GACAGT`	2	--	ut3¹		0	--	--	--	--
rs148836886^1,2		--	25226106(+)	`TGTGCA/GTTAAA`	2	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for RUNX3 (25226002 - 25291612 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for RUNX3
2 Indels: 74413 84138
Human Gene Mutation Database (HGMD): RUNX3

SABiosciences Cancer Mutation PCR Assays

2 SABiosciences qBiomarker Copy Number PCR Arrays containing RUNX3:

Oncogenes & Tumor Suppressor Genes 384HC

Pancreatic Cancer

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RUNX3

DNA2.0 Custom Variant and Variant Library Synthesis for RUNX3

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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RUNX3 for disorders           About GeneDecksing

OMIM gene information: 600210    OMIM disorders: --

20/61 diseases for RUNX3 (see all 61):    About MalaCards

acute myeloid leukemia myeloid leukemia testicular yolk sac tumor cleidocranial dysplasia

leukemia squamous cell carcinoma irritable bowel syndrome biliary tract cancer

barrett's esophagus adenoid cystic carcinoma oral squamous cell carcinoma esophageal squamous cell carcinoma

inflammatory bowel disease papillary thyroid carcinoma basal cell carcinoma intrahepatic cholangiocarcinoma

epithelial ovarian cancer ulcerative colitis mucoepidermoid carcinoma adenoiditis

3 diseases from the University of Copenhagen DISEASES database for RUNX3:

Cleidocranial dysplasia Colorectal cancer Carcinoma

10/28 Novoseek disease relationships for RUNX3 gene (see all 28) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
microsatellite instability	81.1	6	15386381 (1), 19470733 (1), 19789368 (1), 19117505 (1) (see all 5)
gastric cancer	75.4	163	17085650 (7), 15386419 (6), 16140942 (6), 19290488 (6) (see all 49)
colorectal cancer	66.8	51	16080503 (5), 19223906 (3), 15273736 (3), 17270239 (3) (see all 20)
tumors	59.8	174	19336521 (6), 20348954 (5), 15386381 (4), 18410404 (4) (see all 83)
gastric tumor	58.5	7	18772112 (1), 20490322 (1), 20353948 (1), 20492341 (1) (see all 7)
gastric carcinoma	56.9	31	15051926 (6), 20485621 (4), 17956589 (3), 14968123 (3) (see all 10)
colon cancer	54.8	24	15386381 (7), 18949360 (6), 18772112 (1), 14968123 (1) (see all 6)
cancer	54.7	71	17914577 (3), 18639281 (3), 14968123 (3), 18430739 (3) (see all 39)
leukemogenesis	48.6	2	12370805 (1), 12682904 (1)
cleidocranial dysplasia	46.4	1	15138260 (1)

Human Genome Epidemiology (HuGE) Navigator: RUNX3 (17 documents)

Export disorders for RUNX3 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for RUNX3 gene, integrated from 9 sources (see all 330):
(articles sorted by number of sources associating them with RUNX3)

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AML1, AML2, and AML3, the human members of the runt domain gene- family: cDNA structure, expression, and chromosomal localization. (PubMed id 7835892)^{1, 2, 3} Levanon D.... Groner Y. (1994)
Src kinase phosphorylates RUNX3 at tyrosine residues and localizes the protein in the cytoplasm. (PubMed id 20100835)^{1, 2, 9} Goh Y.M....Bae S.C. (2010)
RUNX1 associates with histone deacetylases and SUV39H1 to repress transcription. (PubMed id 16652147)^{1, 2} Reed-Inderbitzin E.... Hiebert S.W. (2006)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{1, 2} Gregory S.G.... Bentley D.R. (2006)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors. (PubMed id 9751710)^{1, 2} Levanon D.... Groner Y. (1998)
Identification of a new murine runt domain-containing gene, Cbfa3, and localization of the human homolog, CBFA3, to chromosome 1p35- pter. (PubMed id 7607690)^{1, 2} Wijmenga C....Collins F.S. (1995)
Cloning, mapping and expression of PEBP2 alpha C, a third gene encoding the mammalian Runt domain. (PubMed id 7622058)^{1, 2} Bae S.-C.... Ito Y. (1995)
Expression of RUNX3 gene, methylation status and clinicopathological significance in breast cancer and breast cancer cell lines. (PubMed id 18580070)^{1, 9} Jiang Y....Geng J. (2008)
Regulation of RUNX3 tumor suppressor gene expression in cutaneous melanoma. (PubMed id 19336521)^{1, 9} Kitago M....Hoon D.S. (2009)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 864	HGNC: 10473	AceView: RUNX3	Ensembl:ENSG00000020633	euGenes: HUgn864
ECgene: RUNX3	H-InvDB: RUNX3

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for RUNX3	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for RUNX3	Genetics and Cytogenetics in Oncology and Haematology

Intellectual Property for RUNX3 gene
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Patent Information for RUNX3 gene:
Search GeneIP for patents involving RUNX3

Licensable Technologies for RUNX3 gene:

Weizmann Institute:

Treating T-cell related inflammatory conditions by targeting Runx3

GeneCards and IP:
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RUNX3 Gene

runt-related transcription factor 3

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RUNX3 (Gene Symbol)
Runt-Related Transcription Factor 3
AML2
CBFA3
PEBP2A3
Acute Myeloid Leukemia 2 Protein
Core-Binding Factor Subunit Alpha-3
Oncogene AML-2
Polyomavirus Enhancer-Binding Protein 2 Alpha C Subunit
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
PEBP2aC
Acute Myeloid Leukemia Gene 2
Core-Binding Factor, Runt Domain, Alpha Subunit 3
PEA2 Alpha C
PEBP2 Alpha C
Transcription Factor AML2

Lymphoma
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GASTRIC CARCINOMA
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Microsatellite Instability
Adenoma
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GASTRIC TUMOR
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Carcinoma
Carcinoma Squamous Cell
ADENOCARCINOMA LUNG
Cervical Cancer
Leukemia
Metaplasia
Breast Cancer
prostate cancer
primary tumor
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HEPATOCELLULAR CARCINOMA
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RUNX3 Gene

runt-related transcription factor 3

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