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RUNX2 RUNX family transcription factor 2 [ Homo sapiens (human) ]

Gene ID: 860, updated on 17-Oct-2021

Summary

Official Symbol
RUNX2provided by HGNC
Official Full Name
RUNX family transcription factor 2provided by HGNC
Primary source
HGNC:HGNC:10472
See related
Ensembl:ENSG00000124813 MIM:600211
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
CCD; AML3; CCD1; CLCD; OSF2; CBFA1; OSF-2; PEA2aA; PEBP2aA; CBF-alpha-1
Summary
This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. Two regions of potential trinucleotide repeat expansions are present in the N-terminal region of the encoded protein, and these and other mutations in this gene have been associated with the bone development disorder cleidocranial dysplasia (CCD). Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Jul 2016]
Expression
Broad expression in bone marrow (RPKM 1.9), appendix (RPKM 1.3) and 23 other tissues See more
Orthologs
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Genomic context

See RUNX2 in Genome Data Viewer
Location:
6p21.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (45328330..45551082)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45296067..45518819)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene SPT3 homolog, SAGA and STAGA complex component Neighboring gene poly(rC) binding protein 2 pseudogene Neighboring gene microRNA 586 Neighboring gene RUNX2 P1 promoter region Neighboring gene runt related transcription factor 2 polyalanine expansion region Neighboring gene Sharpr-MPRA regulatory region 695 Neighboring gene RUNX2 antisense RNA 1 Neighboring gene uncharacterized LOC107986519

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Cleidocranial dysostosis Compare labs
Genome-wide association study of periodontal pathogen colonization.
GeneReviews: Not available
Many sequence variants affecting diversity of adult human height.
GeneReviews: Not available
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
GeneReviews: Not available
Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly
MedGen: C3549874 OMIM: 156510 GeneReviews: Not available
Compare labs

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env In human osteoblast (hOB) cell lines, HIV-1 Gag and gp120 reduce RUNX-2 and PPAR-gamma mRNA expression and activity PubMed
Nef nef HIV-1 Nef downregulates the expression of RUNX2 protein in human mesenchymal stem cells PubMed
Pr55(Gag) gag In human osteoblast (hOB) cell lines, HIV-1 Gag and gp120 reduce RUNX-2 and PPAR-gamma mRNA expression and activity PubMed
Tat tat HIV-1 Tat downregulates the expression of RUNX2 protein in human mesenchymal stem 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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC120022, MGC120023

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in BMP signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cell maturation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to BMP stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chondrocyte development IEA
Inferred from Electronic Annotation
more info
 
involved_in chondrocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in endochondral ossification IEA
Inferred from Electronic Annotation
more info
 
involved_in hemopoiesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
involved_in ossification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in ossification TAS
Traceable Author Statement
more info
PubMed 
involved_in osteoblast development IEA
Inferred from Electronic Annotation
more info
 
involved_in osteoblast differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in osteoblast differentiation TAS
Traceable Author Statement
more info
PubMed 
involved_in osteoblast fate commitment IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of fibroblast growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of ossification IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
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
 
located_in cytosol TAS
Traceable Author Statement
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 
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
runt-related transcription factor 2
Names
PEA2-alpha A
PEBP2-alpha A
SL3-3 enhancer factor 1 alpha A subunit
SL3/AKV core-binding factor alpha A subunit
acute myeloid leukemia 3 protein
core-binding factor, runt domain, alpha subunit 1
oncogene AML-3
osteoblast-specific transcription factor 2
polyomavirus enhancer-binding protein 2 alpha A subunit
runt related transcription factor 2

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.

Genomic

  1. NG_008020.2 RefSeqGene

    Range
    5014..227766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001015051.4NP_001015051.3  runt-related transcription factor 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (b, also known as OSF2/CBF1b) is shorter, compared to isoform a.
    Source sequence(s)
    AL096865, AL161907, AL358135
    Consensus CDS
    CCDS43468.2
    UniProtKB/Swiss-Prot
    Q13950
    Related
    ENSP00000360486.4, ENST00000371432.7
    Conserved Domains (3) summary
    pfam00853
    Location:109230
    Runt; Runt domain
    pfam08504
    Location:408499
    RunxI; Runx inhibition domain
    cl25496
    Location:266459
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  2. NM_001024630.4NP_001019801.3  runt-related transcription factor 2 isoform a

    See identical proteins and their annotated locations for NP_001019801.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a, also known as OSF2/CBFA1a).
    Source sequence(s)
    AL096865, AL161907, AL358135
    Consensus CDS
    CCDS43467.2
    UniProtKB/Swiss-Prot
    Q13950
    Related
    ENSP00000495497.1, ENST00000647337.2
    Conserved Domains (3) summary
    pfam00853
    Location:109230
    Runt; Runt domain
    pfam08504
    Location:430521
    RunxI; Runx inhibition domain
    cl25496
    Location:266481
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  3. NM_001278478.2NP_001265407.1  runt-related transcription factor 2 isoform d

    See identical proteins and their annotated locations for NP_001265407.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 5'-most exon, lacks an in-frame exon in the 3' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AL096865, AL161907, AL358135
    Consensus CDS
    CCDS64443.1
    UniProtKB/TrEMBL
    A0A0D9SEN7, Q32MY8
    Related
    ENSP00000485863.1, ENST00000625924.1
    Conserved Domains (3) summary
    pfam05109
    Location:252445
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam00853
    Location:91217
    Runt; Runt domain
    pfam08504
    Location:394485
    RunxI; Runx inhibition domain
  4. NM_001369405.1NP_001356334.1  runt-related transcription factor 2 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate 5'-most exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (e) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AL096865, AL161907, AL358135
    Related
    ENSP00000352514.5, ENST00000359524.7
    Conserved Domains (3) summary
    pfam05109
    Location:252467
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam00853
    Location:91217
    Runt; Runt domain
    pfam08504
    Location:416507
    RunxI; Runx inhibition domain

RNA

  1. NR_103532.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5'-terminal exon, lacks several exons, and contains an alternate 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region and does not encode a supported protein.
    Source sequence(s)
    AL096865, BX108677
    Related
    ENST00000483243.5
  2. NR_103533.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks several exons, and contains an alternate 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region and does not encode a supported protein.
    Source sequence(s)
    AL096865, AW469546, BX108677

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    45328330..45551082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004348.3: Suppressed sequence

    Description
    NM_004348.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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