Runx2 RUNX family transcription factor 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Runx2provided by RGD
Official Full Name: RUNX family transcription factor 2provided by RGD
Primary source: RGD:2282
See related: EnsemblRapid:ENSRNOG00000020193 AllianceGenome:RGD:2282
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cbfa1; OSF-2; CBF-alpha-1
Summary: Enables DNA-binding transcription factor binding activity; general transcription initiation factor binding activity; and histone deacetylase binding activity. Involved in cellular response to fibroblast growth factor stimulus; osteoblast differentiation; and positive regulation of ossification. Located in nucleus. Human ortholog(s) of this gene implicated in cleidocranial dysplasia and metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome. Orthologous to human RUNX2 (RUNX family transcription factor 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 29.2), Lung (RPKM 17.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q13

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (23661278..23990248)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (16167504..16492826)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (18564743..18773092)

Chromosome 9 - NC_086027.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epigenetic Repression of RUNX2 and OSX Promoters Controls the Nonmineralized State of the Periodontal Ligament.
Title: Epigenetic Repression of RUNX2 and OSX Promoters Controls the Nonmineralized State of the Periodontal Ligament.
Diminished arachidonate 5-lipoxygenase perturbs phase separation and transcriptional response of Runx2 to reverse pathological ventricular remodeling.
Title: Diminished arachidonate 5-lipoxygenase perturbs phase separation and transcriptional response of Runx2 to reverse pathological ventricular remodeling.
Parathyroid Hormone-regulation of Runx2 by MiR-290 for Matrix Metalloproteinase-13 Expression in Rat Osteoblastic Cells.
Title: Parathyroid Hormone-regulation of Runx2 by MiR-290 for Matrix Metalloproteinase-13 Expression in Rat Osteoblastic Cells.
Regulation of transforming growth factor-beta1-stimulation of Runx2 acetylation for matrix metalloproteinase 13 expression in osteoblastic cells.
Title: Regulation of transforming growth factor-β1-stimulation of Runx2 acetylation for matrix metalloproteinase 13 expression in osteoblastic cells.
LncRNA H19 sponges miR-103-3p to promote the high phosphorus-induced osteoblast phenotypic transition of vascular smooth muscle cells by upregulating Runx2.
Title: LncRNA H19 sponges miR-103-3p to promote the high phosphorus-induced osteoblast phenotypic transition of vascular smooth muscle cells by upregulating Runx2.
Induction of cardiomyocyte calcification is dependent on FoxO1/NFATc3/Runx2 signaling.
Title: Induction of cardiomyocyte calcification is dependent on FoxO1/NFATc3/Runx2 signaling.
MiR-320b negatively regulates ovariectomy-induced osteoporosis in rats by decreasing RUNX2.
Title: MiR-320b negatively regulates ovariectomy-induced osteoporosis in rats by decreasing RUNX2.
miRNA320a-3p/RUNX2 signal programming mediates the transgenerational inheritance of inhibited ovarian estrogen synthesis in female offspring rats induced by prenatal dexamethasone exposure.
Title: miRNA320a-3p/RUNX2 signal programming mediates the transgenerational inheritance of inhibited ovarian estrogen synthesis in female offspring rats induced by prenatal dexamethasone exposure.
Spatio-temporal immunolocalization of VEGF-A, Runx2, and osterix during the early steps of intramembranous ossification of the alveolar process in rat embryos.
Title: Spatio-temporal immunolocalization of VEGF-A, Runx2, and osterix during the early steps of intramembranous ossification of the alveolar process in rat embryos.
Cbfa1 expression in vascular smooth muscle cells may be elevated by increased nitric oxide/iNOS.
Title: Cbfa1 expression in vascular smooth muscle cells may be elevated by increased nitric oxide/iNOS.

Submit: New GeneRIF Correction See all GeneRIFs (98)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC150810P1 (e-PCR)
- UniSTS:271104

Runx2 (e-PCR), detects polymorphism
- UniSTS:280406

Runx2 (e-PCR), detects polymorphism
- UniSTS:547959

AF029259 (e-PCR)
- UniSTS:32376

Runx2 (e-PCR), detects polymorphism
- UniSTS:547303

BE116846 (e-PCR)
- UniSTS:248552

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables bHLH transcription factor binding	IEA Inferred from Electronic Annotation more info
enables bHLH transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables general transcription initiation factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in BMP signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in SMAD protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in SMAD protein signal transduction	ISO Inferred from Sequence Orthology more info
involved_in T cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in bone mineralization	IEA Inferred from Electronic Annotation more info
acts_upstream_of bone mineralization	ISO Inferred from Sequence Orthology more info
involved_in cell maturation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell maturation	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fibroblast growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to zinc ion starvation	IEP Inferred from Expression Pattern more info	PubMed
involved_in chondrocyte development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chondrocyte development	ISO Inferred from Sequence Orthology more info
acts_upstream_of chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in embryonic cranial skeleton morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endochondral ossification	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_positive_effect gene expression	ISO Inferred from Sequence Orthology more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
involved_in ligamentous ossification	IEA Inferred from Electronic Annotation more info
involved_in ligamentous ossification	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in odontogenesis of dentin-containing tooth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within odontogenesis of dentin-containing tooth	ISO Inferred from Sequence Orthology more info
involved_in osteoblast development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within osteoblast development	ISO Inferred from Sequence Orthology more info
involved_in osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in osteoblast fate commitment	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within osteoblast fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of developmental process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of multicellular organismal process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ossification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of osteoblast differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of osteoblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of stem cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of fibroblast growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of fibroblast growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of odontogenesis of dentin-containing tooth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of odontogenesis of dentin-containing tooth	ISO Inferred from Sequence Orthology more info
involved_in regulation of ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of ossification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of osteoblast differentiation	TAS Traceable Author Statement more info	PubMed
involved_in response to insulin	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to sodium phosphate	IEA Inferred from Electronic Annotation more info
involved_in response to sodium phosphate	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in stem cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in stem cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of stem cell proliferation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of chromatin	IEA Inferred from Electronic Annotation more info
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: runt-related transcription factor 2

Names: core-binding factor subunit alpha-1; osteoblast-specific 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.

mRNA and Protein(s)

NM_001278483.2 → NP_001265412.1 runt-related transcription factor 2 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A8I6AS80

Conserved Domains (2) summary

pfam00853
Location:117 → 238

Runt; Runt domain

pfam08504
Location:438 → 529

RunxI; Runx inhibition domain
NM_001278484.3 → NP_001265413.1 runt-related transcription factor 2 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A8I6AS80

Related

ENSRNOP00000077713.1, ENSRNOT00000098417.2

Conserved Domains (3) summary

pfam05109
Location:260 → 475

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

pfam00853
Location:96 → 224

Runt; Runt domain

pfam08504
Location:424 → 515

RunxI; Runx inhibition domain
NM_001415755.1 → NP_001402684.1 runt-related transcription factor 2 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A8I6AS80

Related

ENSRNOP00000057733.4, ENSRNOT00000061014.6

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

23661278..23990248

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083955.2 → XP_038939883.1 runt-related transcription factor 2 isoform X3

UniProtKB/TrEMBL

A0A8I6G3M7

Related

ENSRNOP00000079713.2, ENSRNOT00000104855.2

Conserved Domains (2) summary

PHA03247
Location:294 → 581

PHA03247; large tegument protein UL36; Provisional

pfam00853
Location:192 → 318

Runt; Runt domain
XM_039083956.2 → XP_038939884.1 runt-related transcription factor 2 isoform X4

UniProtKB/TrEMBL

A0A8I6G3M7

Conserved Domains (2) summary

PHA03247
Location:283 → 570

PHA03247; large tegument protein UL36; Provisional

pfam00853
Location:181 → 307

Runt; Runt domain
XM_063267498.1 → XP_063123568.1 runt-related transcription factor 2 isoform X9

UniProtKB/TrEMBL

A0A8I5ZNG8, F1M9C5

Related

ENSRNOP00000079678.1, ENSRNOT00000097660.2
XM_039083954.2 → XP_038939882.1 runt-related transcription factor 2 isoform X1

UniProtKB/TrEMBL

A0A8I6G3M7

Conserved Domains (2) summary

PHA03247
Location:319 → 606

PHA03247; large tegument protein UL36; Provisional

pfam00853
Location:217 → 343

Runt; Runt domain
XM_039083957.2 → XP_038939885.1 runt-related transcription factor 2 isoform X6

UniProtKB/TrEMBL

A0A8I6G3M7

Conserved Domains (2) summary

PHA03247
Location:339 → 548

PHA03247; large tegument protein UL36; Provisional

pfam00853
Location:217 → 343

Runt; Runt domain
XM_006244549.5 → XP_006244611.1 runt-related transcription factor 2 isoform X2

See identical proteins and their annotated locations for XP_006244611.1

UniProtKB/TrEMBL

A0A8I6AS80, A6JJ12

Related

ENSRNOP00000110394.1, ENSRNOT00000126566.1

Conserved Domains (2) summary

pfam00853
Location:221 → 342

Runt; Runt domain

pfam08504
Location:542 → 633

RunxI; Runx inhibition domain
XM_017596547.3 → XP_017452036.1 runt-related transcription factor 2 isoform X5

UniProtKB/TrEMBL

A0A8I6AS80

Related

ENSRNOP00000097985.2, ENSRNOT00000116490.2
XM_017596548.3 → XP_017452037.1 runt-related transcription factor 2 isoform X7

UniProtKB/TrEMBL

F1M9C5
XM_017596549.3 → XP_017452038.1 runt-related transcription factor 2 isoform X8

UniProtKB/TrEMBL

A0A8I6AS80
XM_017596551.3 → XP_017452040.1 runt-related transcription factor 2 isoform X10

UniProtKB/TrEMBL

A0A8I6AS80
XM_006244554.5 → XP_006244616.1 runt-related transcription factor 2 isoform X11

UniProtKB/TrEMBL

A0A8I5Y1Y1

Conserved Domains (2) summary

pfam00853
Location:103 → 223

Runt; Runt domain

pfam08504
Location:366 → 457

RunxI; Runx inhibition domain
XM_017596552.3 → XP_017452041.1 runt-related transcription factor 2 isoform X12

UniProtKB/TrEMBL

A0A8I5Y1Y1

RNA

XR_010054619.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_053470.2: Suppressed sequence

Description

NM_053470.2: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.