RUNX3 runt-related transcription factor 3 [Homo sapiens] - Gene

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Summary

Official Symbol: RUNX3provided by HGNC
Official Full Name: runt-related transcription factor 3provided by HGNC
Primary source: HGNC:10473
Locus tag: RP3-398I9.1
See related: Ensembl:ENSG00000020633; HPRD:02565; 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; FLJ34510; MGC16070
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. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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Genomic context

Location :: 1p36

Sequence :: Chromosome: 1; NC_000001.10 (25226002..25291501, complement)

See RUNX3 in Epigenomics, MapViewer

Chromosome 1 - NC_000001.10 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

ROS silenced the tumor suppressor, RUNX3, by epigenetic regulation and may therefore be associated with the progression of colorectal cancer
Title: Epigenetic changes induced by oxidative stress in colorectal cancer cells: methylation of tumor suppressor RUNX3.
Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor.
Title: Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor.
RUNX3 deregulation is associated with Helicobacter pylori-induced pathogenesis and development of intestinal metaplasia.
Title: Phosphorylation of the gastric tumor suppressor RUNX3 following H. pylori infection results in its localization to the cytoplasm.
RUNX3 plays a pivotal role in 5-aza-CdR- and TSA-induced cell proliferation and apoptosis in K562 and Reh cells.
Title: RUNX3 is involved in caspase-3-dependent apoptosis induced by a combination of 5-aza-CdR and TSA in leukaemia cell lines.
Promoter methylation might be one of the important factors of RUNX3 inactivation, and might play an important role in carcinogenesis and progression of papillary thyroid carcinoma.
Title: [Methylation and expression of RUNX3 gene promoter in papillary thyroid carcinoma].
The serum RUNX3 promoter hypermethylation may be a promising biomarker for the early diagnosis of esophageal squamous cell carcinoma (ESCC), gastric cancer (GC) and colorectal cancer (CRC) patients.
Title: Analysis of the RUNX3 gene methylation in serum DNA from esophagus squamous cell carcinoma, gastric and colorectal adenocarcinoma patients.
Consistent with its ability to regulate the levels of ERalpha, expression of RUNX3 inversely correlates with the expression of ERalpha in breast cancer cell lines, human breast cancer tissues and Runx3(+/-) mouse mammary tumors
Title: RUNX3 acts as a tumor suppressor in breast cancer by targeting estrogen receptor α.
RUNX3 methylation is associated with disease progression in patients with non-muscle-invasive bladder cancer.
Title: RUNX3 methylation as a predictor for disease progression in patients with non-muscle-invasive bladder cancer.
Abnormal expression of Ezh2, Runx3 and caspase-3 is associated with the development and progression of endometrioid adenocarcinoma.
Title: [Expression and relationship of Ezh2, Runx3 and caspase-3 in endometrial adenocarcinoma].
determined that the tumor suppressors CLU, NGFR, and RUNX3 were also directly repressed by EZH2 like CASZ1 in NB cells
Title: EZH2 Mediates epigenetic silencing of neuroblastoma suppressor genes CASZ1, CLU, RUNX3, and NGFR.

Submit: New GeneRIF Correction See all (151)

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

Multiple common variants for celiac disease influencing immune gene expression.

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Products	Interactant	Other Gene	Source	Pubs	Description
NP_004341.1	NP_001746.1	CBFB	BIND	PubMed	Cbf-beta interacts with AML2. This interaction was modeled on a demonstrated interaction between mouse Cbf-beta and human AML2.
NP_004341.1	NP_005068.2	TLE1	BIND	PubMed	AML2 interacts with TLE1.
Q13761	Q13951	CBFB	HPRD	PubMed
Q13761	Q09472	EP300	HPRD	PubMed
Q13761	Q13547	HDAC1	HPRD	PubMed
Q13761	Q92769	HDAC2	HPRD	PubMed
Q13761	P56524	HDAC4	HPRD	PubMed
Q13761	Q9UQL6	HDAC5	HPRD	PubMed
Q13761	P84022	SMAD3	HPRD	PubMed
Q13761	Q9HCE7	SMURF1	HPRD	PubMed
Q13761	Q9HAU4	SMURF2	HPRD	PubMed
Q13761	Q04724	TLE1	HPRD	PubMed
BioGRID:107312	BioGRID:107313	CBFB	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:198645	Cdk4	BioGRID	PubMed	Biochemical Activity
BioGRID:107312	BioGRID:108347	EP300	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:108446	EZH2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:115083	HDAC9	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:110358	MDM2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:110913	NOTCH1	BioGRID	PubMed	Affinity Capture-Western; Co-localization; Reconstituted Complex
BioGRID:107312	BioGRID:116459	PHB2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:107312	BioGRID:109736	RBPJ	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:116593	SIRT2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:110261	SMAD1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:110262	SMAD2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:110263	SMAD3	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:110265	SMAD5	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:121411	SMURF1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:122265	SMURF2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:109657	SP110	BioGRID	PubMed	Two-hybrid
BioGRID:107312	BioGRID:112706	SUV39H1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:112943	TLE1	BioGRID	PubMed	Far Western; Two-hybrid
BioGRID:107312	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western
BioGRID:107312	BioGRID:246986	Vdr	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107312	BioGRID:115684	YAP1	BioGRID	PubMed	Reconstituted Complex

Function	Evidence Code	Pubs
ATP binding	NAS Non-traceable Author Statement more info	PubMed
DNA binding	IEA Inferred from Electronic Annotation more info
RNA polymerase II regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
sequence-specific DNA binding RNA polymerase II transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
sequence-specific DNA binding transcription factor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
induction of apoptosis	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 from RNA polymerase II promoter	ISS Inferred from Sequence or Structural Similarity more info
peripheral nervous system neuron development	TAS Traceable Author Statement more info
protein phosphorylation	IDA Inferred from Direct Assay more info
regulation of transcription, DNA-dependent	NAS Non-traceable Author Statement more info	PubMed
regulation of transcription, DNA-dependent	TAS Traceable Author Statement more info	PubMed
transcription from RNA polymerase II promoter	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
cytoplasm	IDA Inferred from Direct Assay more info
nuclear chromatin	ISS Inferred from Sequence or Structural Similarity more info
nucleus	IDA Inferred from Direct Assay more info

General protein information

Preferred Names: runt-related transcription factor 3

Names: runt-related transcription factor 3; CBF-alpha-3; PEA2 alpha C; PEA2-alpha C; PEBP2 alpha C; PEBP2-alpha C; oncogene AML-2; transcription factor AML2; acute myeloid leukemia gene 2; acute myeloid leukemia 2 protein; core-binding factor subunit alpha-3; SL3-3 enhancer factor 1 alpha C subunit; SL3/AKV core-binding factor alpha C subunit; core-binding factor, runt domain, alpha subunit 3; polyomavirus enhancer-binding protein 2 alpha C subunit

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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)

NM_001031680.2 → NP_001026850.1 runt-related transcription factor 3 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as p46, represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AI375031, AL023096, BC013362, DA935726

Consensus CDS

CCDS30633.1

UniProtKB/TrEMBL

B1AJV5

UniProtKB/Swiss-Prot

Q13761

Related

ENSP00000382800, ENST00000399916

Conserved Domains (3) summary

pfam00853
Location:67 – 200
Blast Score: 683

Runt; Runt domain

pfam08504
Location:327 – 429
Blast Score: 326

RunxI; Runx inhibition domain

PHA03247
Location:191 – 325
Blast Score: 86

PHA03247; large tegument protein UL36; Provisional
NM_004350.2 → NP_004341.1 runt-related transcription factor 3 isoform 2

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, OTTHUMP00000003370, ENST00000308873, OTTHUMT00000009284

Conserved Domains (3) summary

pfam00853
Location:53 – 186
Blast Score: 682

Runt; Runt domain

pfam08504
Location:313 – 415
Blast Score: 327

RunxI; Runx inhibition domain

PHA03247
Location:177 – 311
Blast Score: 86

PHA03247; large tegument protein UL36; Provisional

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000001.10 Reference GRCh37.p5 Primary Assembly

Range

25226002..25291501, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000133.1 Alternate HuRef

Range

23479020..23544351, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AJ238394.1	CAB42882.1
genomic	AL023096.1	CAA18856.1
		CAI20422.1
genomic	AL023096.1	CAA18856.1
		CAI20422.1
genomic	AL445471.13	CAC42093.2
genomic	CH471134.1	EAW95147.1
		EAW95148.1
		EAW95149.1
genomic	CQ834770.1	CAH05600.1
genomic	FB571463.1	CAR95149.1
genomic	FB571465.1	CAR95150.1
genomic	HI574042.1	CBX47510.1
genomic	HI574044.1	CBX47511.1
genomic	U14520.1	AAA86465.1
genomic	Z38104.1	None
genomic	Z38108.1	None
mRNA	AF022726.2	AAB80759.2
mRNA	AI375031.1	None
mRNA	AJ001432.1	None
mRNA	AK091829.1	None
mRNA	AK300056.1	BAG61865.1
mRNA	AK301044.1	BAG62657.1
mRNA	AK310945.1	None
mRNA	BC013362.2	AAH13362.1
mRNA	DA935726.1	None
mRNA	X79550.2	CAA56093.2
mRNA	Z35278.1	CAA84541.1

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
O14814	GenPept	UniProtKB/TrEMBL:O14814
Q13761.2	GenPept	UniProtKB/Swiss-Prot:Q13761
Q9Y3R8	GenPept	UniProtKB/TrEMBL:Q9Y3R8