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Runx2 runt-related transcription factor 2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 367218, updated on 12-Aug-2018

Summary

Official Symbol
Runx2provided by RGD
Official Full Name
runt-related transcription factor 2provided by RGD
Primary source
RGD:2282
See related
Ensembl:ENSRNOG00000020193
Gene type
protein coding
RefSeq status
PROVISIONAL
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
Expression
Biased expression in Spleen (RPKM 29.2), Lung (RPKM 17.9) and 9 other tissues See more
Orthologs

Genomic context

See Runx2 in Genome Data Viewer
Location:
9q13
Exon count:
9
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (18564743..18773092)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 9 NC_005108.3 (17448142..17658373)

Chromosome 9 - NC_005108.4Genomic Context describing neighboring genes Neighboring gene similar to CG8435-PA Neighboring gene SPT3 homolog, SAGA and STAGA complex component Neighboring gene zinc ribbon domain containing 1 antisense Neighboring gene uncharacterized LOC103690503 Neighboring gene uncharacterized LOC108351894

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

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

General protein information

Preferred Names
runt-related transcription factor 2
Names
CBF-alpha-1
core-binding factor subunit alpha-1
osteoblast-specific transcription factor 2

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)

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

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AABR07066834, AABR07066837, AABR07066838
    UniProtKB/TrEMBL
    F1M9C5
    Related
    ENSRNOP00000057733.3, ENSRNOT00000061014.4
    Conserved Domains (2) summary
    pfam00853
    Location:117238
    Runt; Runt domain
    pfam08504
    Location:438529
    RunxI; Runx inhibition domain
  2. NM_001278484.2NP_001265413.1  runt-related transcription factor 2 isoform 2

    Status: PROVISIONAL

    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)
    AABR07066834, AABR07066837, AABR07066838
    Conserved Domains (2) summary
    pfam00853
    Location:103224
    Runt; Runt domain
    pfam08504
    Location:424515
    RunxI; Runx inhibition domain

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005108.4 Reference Rnor_6.0 Primary Assembly

    Range
    18564743..18773092
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006244550.3XP_006244612.1  runt-related transcription factor 2 isoform X3

    Conserved Domains (2) summary
    pfam00853
    Location:196317
    Runt; Runt domain
    pfam08504
    Location:517608
    RunxI; Runx inhibition domain
  2. XM_006244551.3XP_006244613.1  runt-related transcription factor 2 isoform X4

    Conserved Domains (2) summary
    pfam00853
    Location:185306
    Runt; Runt domain
    pfam08504
    Location:506597
    RunxI; Runx inhibition domain
  3. XM_006244549.3XP_006244611.1  runt-related transcription factor 2 isoform X1

    See identical proteins and their annotated locations for XP_006244611.1

    Conserved Domains (2) summary
    pfam00853
    Location:221342
    Runt; Runt domain
    pfam08504
    Location:542633
    RunxI; Runx inhibition domain
  4. XM_017596547.1XP_017452036.1  runt-related transcription factor 2 isoform X2

  5. XM_017596548.1XP_017452037.1  runt-related transcription factor 2 isoform X5

  6. XM_017596549.1XP_017452038.1  runt-related transcription factor 2 isoform X6

  7. XM_017596551.1XP_017452040.1  runt-related transcription factor 2 isoform X7

  8. XM_006244554.3XP_006244616.1  runt-related transcription factor 2 isoform X8

    Conserved Domains (2) summary
    pfam00853
    Location:103223
    Runt; Runt domain
    pfam08504
    Location:366457
    RunxI; Runx inhibition domain
  9. XM_017596552.1XP_017452041.1  runt-related transcription factor 2 isoform X9

Alternate Rn_Celera

Genomic

  1. AC_000077.1 Alternate Rn_Celera

    Range
    13904221..14111920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. 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.
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