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RUNX2 runt related transcription factor 2 [ Homo sapiens (human) ]

Gene ID: 860, updated on 22-Oct-2017
Official Symbol
RUNX2provided by HGNC
Official Full Name
runt related transcription factor 2provided by HGNC
Primary source
HGNC:HGNC:10472
See related
Ensembl:ENSG00000124813 MIM:600211; Vega:OTTHUMG00000014774
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]
Orthologs
Location:
6p21.1
Exon count:
16
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (45328142..45664032)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45296054..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 antisense RNA 1 Neighboring gene uncharacterized LOC107986519 Neighboring gene uncharacterized LOC105375078 Neighboring gene chloride intracellular channel 5

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Cleidocranial dysostosis
MedGen: C0008928 OMIM: 119600 GeneReviews: Cleidocranial Dysplasia
Compare labs
Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly
MedGen: C1834969 OMIM: 156510 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of periodontal pathogen colonization.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

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

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC120022, MGC120023

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II core promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
bHLH transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
repressing transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
transcription factor activity, sequence-specific DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
BMP signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cell maturation IEA
Inferred from Electronic Annotation
more info
 
cellular response to BMP stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
chondrocyte development IEA
Inferred from Electronic Annotation
more info
 
chondrocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
endochondral ossification IEA
Inferred from Electronic Annotation
more info
 
hemopoiesis IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
ossification TAS
Traceable Author Statement
more info
PubMed 
osteoblast development IEA
Inferred from Electronic Annotation
more info
 
osteoblast differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
osteoblast differentiation TAS
Traceable Author Statement
more info
PubMed 
osteoblast fate commitment IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
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
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
regulation of fibroblast growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription from RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
more info
 
stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 
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

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_008020.1 RefSeqGene

    Range
    5001..227766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001015051.3NP_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 (2) summary
    pfam00853
    Location:109230
    Runt; Runt domain
    pfam08504
    Location:408499
    RunxI; Runx inhibition domain
  2. NM_001024630.3NP_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) represents the longest transcript and 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
    ENSP00000420707.2, OTTHUMP00000016533, ENST00000465038.6, OTTHUMT00000040754
    Conserved Domains (2) summary
    pfam00853
    Location:109230
    Runt; Runt domain
    pfam08504
    Location:430521
    RunxI; Runx inhibition domain
  3. NM_001278478.1NP_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)
    AL161907, BC108919, DR005078
    Consensus CDS
    CCDS64443.1
    UniProtKB/TrEMBL
    A0A0D9SEN7, Q32MY8
    Related
    ENSP00000485863.1, OTTHUMP00000279213, ENST00000625924.1, OTTHUMT00000484119
    Conserved Domains (2) summary
    pfam00853
    Location:95216
    Runt; Runt domain
    pfam08504
    Location:394485
    RunxI; Runx inhibition domain

RNA

  1. NR_103532.1 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, AW469546, BX108677
    Related
    ENST00000483243.5
  2. NR_103533.1 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 Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

    Range
    45328142..45664032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011391.1XP_016866880.1  runt-related transcription factor 2 isoform X2

  2. XM_011514960.2XP_011513262.1  runt-related transcription factor 2 isoform X1

    Conserved Domains (1) summary
    pfam00853
    Location:177298
    Runt; Runt domain
  3. XM_011514963.2XP_011513265.1  runt-related transcription factor 2 isoform X5

    Conserved Domains (1) summary
    pfam00853
    Location:177297
    Runt; Runt domain
  4. XM_011514961.2XP_011513263.1  runt-related transcription factor 2 isoform X3

    Conserved Domains (2) summary
    pfam00853
    Location:177298
    Runt; Runt domain
    pfam08504
    Location:498589
    RunxI; Runx inhibition domain
  5. XM_011514964.2XP_011513266.1  runt-related transcription factor 2 isoform X7

    Conserved Domains (1) summary
    pfam00853
    Location:177298
    Runt; Runt domain
  6. XM_011514962.2XP_011513264.1  runt-related transcription factor 2 isoform X4

    Conserved Domains (2) summary
    pfam00853
    Location:177298
    Runt; Runt domain
    pfam08504
    Location:476567
    RunxI; Runx inhibition domain
  7. XM_017011393.1XP_016866882.1  runt-related transcription factor 2 isoform X9

  8. XM_011514965.2XP_011513267.1  runt-related transcription factor 2 isoform X10

    Conserved Domains (1) summary
    pfam00853
    Location:177298
    Runt; Runt domain
  9. XM_017011394.1XP_016866883.1  runt-related transcription factor 2 isoform X12

  10. XM_017011395.1XP_016866884.1  runt-related transcription factor 2 isoform X13

  11. XM_017011392.1XP_016866881.1  runt-related transcription factor 2 isoform X6

    Related
    ENSP00000458178.1, OTTHUMP00000257615, ENST00000576263.5, OTTHUMT00000438832
  12. XM_006715232.1XP_006715295.1  runt-related transcription factor 2 isoform X8

    See identical proteins and their annotated locations for XP_006715295.1

    Conserved Domains (2) summary
    pfam00853
    Location:95215
    Runt; Runt domain
    pfam08504
    Location:358449
    RunxI; Runx inhibition domain
  13. XM_017011396.1XP_016866885.1  runt-related transcription factor 2 isoform X14

    UniProtKB/TrEMBL
    I3L354
    Related
    ENSP00000460188.1, OTTHUMP00000257616, ENST00000478660.6, OTTHUMT00000438833
  14. XM_011514966.2XP_011513268.1  runt-related transcription factor 2 isoform X11

    Conserved Domains (1) summary
    pfam00853
    Location:174
    Runt; Runt domain

RNA

  1. XR_926323.2 RNA Sequence

  2. XR_001743701.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018917.2 Alternate CHM1_1.1

    Range
    45298649..45521390
    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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