Mouse Gene Cebpa (ENSMUST00000042985.10) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus CCAAT/enhancer binding protein (C/EBP), alpha (Cebpa), transcript variant 1, mRNA. (from RefSeq NM_007678)
RefSeq Summary (NM_001287523): This intronless gene encodes a transcription factor that contains a basic leucine zipper (bZIP) domain and recognizes the CCAAT motif in the promoters of target genes. The encoded protein functions in homodimers and also heterodimers with CCAAT/enhancer-binding proteins beta and gamma. Activity of this protein can modulate the expression of genes involved in cell cycle regulation as well as in body weight homeostasis. The use of alternative in-frame non-AUG (CUG) and AUG start codons results in several protein isoforms with different lengths. Differential translation initiation is mediated by an out-of-frame, upstream open reading frame which is located between the CUG and the first AUG start codons. [provided by RefSeq, Sep 2014].
Gencode Transcript: ENSMUST00000042985.10
Gencode Gene: ENSMUSG00000034957.10
Transcript (Including UTRs)
   Position: mm10 chr7:35,119,303-35,121,928 Size: 2,626 Total Exon Count: 1 Strand: +
Coding Region
   Position: mm10 chr7:35,119,419-35,120,498 Size: 1,080 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:35,119,303-35,121,928)mRNA (may differ from genome)Protein (359 aa)
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PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CEBPA_MOUSE
DESCRIPTION: RecName: Full=CCAAT/enhancer-binding protein alpha; Short=C/EBP alpha;
FUNCTION: C/EBP is a DNA-binding protein that recognizes two different motifs: the CCAAT homology common to many promoters and the enhanced core homology common to many enhancers.
SUBUNIT: Interacts with UBN1 (By similarity). Binds DNA as a dimer and can form stable heterodimers with C/EBP beta and gamma. Interacts with PRDM16. Interacts with ZNF638; this interaction increases transcriptional activation.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the bZIP family. C/EBP subfamily.
SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -59.20116-0.510 Picture PostScript Text
3' UTR -580.501430-0.406 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004827 - bZIP
IPR016468 - CCAAT/enhancer-binding

Pfam Domains:
PF07716 - Basic region leucine zipper

SCOP Domains:
75704 - Mitotic arrest deficient-like 1, Mad1
57959 - Leucine zipper domain

ModBase Predicted Comparative 3D Structure on P53566
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsemblEnsembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0001013 RNA polymerase I regulatory region DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0019900 kinase binding
GO:0019904 protein domain specific binding
GO:0042803 protein homodimerization activity
GO:0042826 histone deacetylase binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0044877 macromolecular complex binding
GO:0046982 protein heterodimerization activity
GO:0071837 HMG box domain binding

Biological Process:
GO:0000050 urea cycle
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001889 liver development
GO:0001892 embryonic placenta development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006360 transcription from RNA polymerase I promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007005 mitochondrion organization
GO:0007219 Notch signaling pathway
GO:0007275 multicellular organism development
GO:0008203 cholesterol metabolic process
GO:0008285 negative regulation of cell proliferation
GO:0019221 cytokine-mediated signaling pathway
GO:0030099 myeloid cell differentiation
GO:0030225 macrophage differentiation
GO:0030324 lung development
GO:0030851 granulocyte differentiation
GO:0042127 regulation of cell proliferation
GO:0042593 glucose homeostasis
GO:0045444 fat cell differentiation
GO:0045600 positive regulation of fat cell differentiation
GO:0045669 positive regulation of osteoblast differentiation
GO:0045786 negative regulation of cell cycle
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0045945 positive regulation of transcription from RNA polymerase III promoter
GO:0048469 cell maturation
GO:0048839 inner ear development
GO:0050872 white fat cell differentiation
GO:0050873 brown fat cell differentiation
GO:0055088 lipid homeostasis
GO:0071285 cellular response to lithium ion
GO:0071356 cellular response to tumor necrosis factor
GO:0071407 cellular response to organic cyclic compound
GO:2000144 positive regulation of DNA-templated transcription, initiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005730 nucleolus
GO:0016363 nuclear matrix
GO:0032991 macromolecular complex
GO:0035189 Rb-E2F complex
GO:0036488 CHOP-C/EBP complex
GO:0043231 intracellular membrane-bounded organelle
GO:0090575 RNA polymerase II transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  LF202712 - JP 2014500723-A/10215: Polycomb-Associated Non-Coding RNAs.
LF196219 - JP 2014500723-A/3722: Polycomb-Associated Non-Coding RNAs.
LF204882 - JP 2014500723-A/12385: Polycomb-Associated Non-Coding RNAs.
BC028890 - Mus musculus CCAAT/enhancer binding protein (C/EBP), alpha, mRNA (cDNA clone MGC:19302 IMAGE:4160963), complete cds.
BC011118 - Mus musculus CCAAT/enhancer binding protein (C/EBP), alpha, mRNA (cDNA clone MGC:18705 IMAGE:4194023), complete cds.
BC051102 - Mus musculus CCAAT/enhancer binding protein (C/EBP), alpha, mRNA (cDNA clone MGC:58988 IMAGE:5051761), complete cds.
BC058161 - Mus musculus CCAAT/enhancer binding protein (C/EBP), alpha, mRNA (cDNA clone MGC:65349 IMAGE:5053056), complete cds.
AK155281 - Mus musculus NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630214A13 product:CCAAT/enhancer binding protein (C/EBP), alpha, full insert sequence.
LF203730 - JP 2014500723-A/11233: Polycomb-Associated Non-Coding RNAs.
LF292189 - JP 2014500723-A/99692: Polycomb-Associated Non-Coding RNAs.
BC106174 - Mus musculus cDNA clone IMAGE:5101547.
AK160443 - Mus musculus 10 day old male pancreas cDNA, RIKEN full-length enriched library, clone:1810013I12 product:CCAAT/enhancer binding protein (C/EBP), alpha, full insert sequence.
MA438289 - JP 2018138019-A/10215: Polycomb-Associated Non-Coding RNAs.
MA431796 - JP 2018138019-A/3722: Polycomb-Associated Non-Coding RNAs.
MA440459 - JP 2018138019-A/12385: Polycomb-Associated Non-Coding RNAs.
MA439307 - JP 2018138019-A/11233: Polycomb-Associated Non-Coding RNAs.
MA527766 - JP 2018138019-A/99692: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu05200 - Pathways in cancer
mmu05221 - Acute myeloid leukemia

BioCarta from NCI Cancer Genome Anatomy Project
m_mapkPathway - MAPKinase Signaling Pathway
m_keratinocytePathway - Keratinocyte Differentiation

-  Other Names for This Gene
  Alternate Gene Symbols: CEBPA_MOUSE, NM_007678, P53566, Q91XB6, uc009gjl.1, uc009gjl.2, uc009gjl.3, uc009gjl.4
UCSC ID: uc009gjl.4
RefSeq Accession: NM_001287523
Protein: P53566 (aka CEBPA_MOUSE)
CCDS: CCDS21145.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.