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

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association between the methylations of RUNX3 in peripheral blood and lung cancer: a case-control study.
Title: Association between the methylations of RUNX3 in peripheral blood and lung cancer: a case-control study.
USP7 promotes IgA class switching through stabilizing RUNX3 for germline transcription activation.
Title: USP7 promotes IgA class switching through stabilizing RUNX3 for germline transcription activation.
Runx3 is required for oncogenic Myc upregulation in p53-deficient osteosarcoma.
Title: Runx3 is required for oncogenic Myc upregulation in p53-deficient osteosarcoma.
RUNX3 exerts tumor-suppressive role through inhibiting EXOSC4 expression.
Title: RUNX3 exerts tumor-suppressive role through inhibiting EXOSC4 expression.
Downregulation of lncRNA MIR17HG reduced tumorigenicity and Treg-mediated immune escape of non-small-cell lung cancer cells through targeting the miR-17-5p/RUNX3 axis.
Title: Downregulation of lncRNA MIR17HG reduced tumorigenicity and Treg-mediated immune escape of non-small-cell lung cancer cells through targeting the miR-17-5p/RUNX3 axis.
Ubiquitylation of RUNX3 by RNA-binding ubiquitin ligase MEX3C promotes tumorigenesis in lung adenocarcinoma.
Title: Ubiquitylation of RUNX3 by RNA-binding ubiquitin ligase MEX3C promotes tumorigenesis in lung adenocarcinoma.
RUNX3 inhibits KSHV lytic replication by binding to the viral genome and repressing transcription.
Title: RUNX3 inhibits KSHV lytic replication by binding to the viral genome and repressing transcription.
Differential Runx3, Eomes, and T-bet expression subdivides MS-associated CD4[+] T cells with brain-homing capacity.
Title: Differential Runx3, Eomes, and T-bet expression subdivides MS-associated CD4(+) T cells with brain-homing capacity.
Aberrant Upregulation of RUNX3 Activates Developmental Genes to Drive Metastasis in Gastric Cancer.
Title: Aberrant Upregulation of RUNX3 Activates Developmental Genes to Drive Metastasis in Gastric Cancer.
Down-regulation of EZH2 genes targeting RUNX3 affects proliferation, invasion, and metastasis of human colon cancer cells by Wnt/beta-catenin signaling pathway.
Title: Down-regulation of EZH2 genes targeting RUNX3 affects proliferation, invasion, and metastasis of human colon cancer cells by Wnt/β-catenin signaling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (388)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70984 (e-PCR)
- UniSTS:66570

RH120480 (e-PCR)
- UniSTS:133645

SHGC-74399 (e-PCR)
- UniSTS:76814

Runx3 (e-PCR), detects polymorphism
- UniSTS:463955

D1S1460 (e-PCR)
- UniSTS:149656

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

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

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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)

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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

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:76 → 197

Runt; Runt domain

pfam08504
Location:330 → 429

RunxI; Runx inhibition domain

cl26464
Location:191 → 325

Atrophin-1; Atrophin-1 family
NM_001320672.1 → NP_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:76 → 197

Runt; Runt domain

pfam08504
Location:330 → 429

RunxI; Runx inhibition domain

cl26464
Location:191 → 325

Atrophin-1; Atrophin-1 family
NM_004350.3 → NP_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:62 → 183

Runt; Runt domain

pfam08504
Location:316 → 415

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

24899511..24965138 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005246024.5 → XP_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:76 → 197

Runt; Runt domain

pfam08504
Location:330 → 429

RunxI; Runx inhibition domain

cl26464
Location:191 → 325

Atrophin-1; Atrophin-1 family
XM_047433131.1 → XP_047289087.1 runt-related transcription factor 3 isoform X1

UniProtKB/TrEMBL

B4DVE5
XM_011542351.2 → XP_011540653.1 runt-related transcription factor 3 isoform X2

UniProtKB/TrEMBL

B4DVE5

Conserved Domains (2) summary

pfam00853
Location:76 → 196

Runt; Runt domain

pfam08504
Location:277 → 376

RunxI; Runx inhibition domain

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

24735232..24800883 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339349.1 → XP_054195324.1 runt-related transcription factor 3 isoform X1

UniProtKB/TrEMBL

B4DVE5
XM_054339350.1 → XP_054195325.1 runt-related transcription factor 3 isoform X2

UniProtKB/TrEMBL

B4DVE5