Mouse Gene Nr2e1 (ENSMUST00000019938.10) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus nuclear receptor subfamily 2, group E, member 1 (Nr2e1), mRNA. (from RefSeq NM_152229)
Gencode Transcript: ENSMUST00000019938.10
Gencode Gene: ENSMUSG00000019803.11
Transcript (Including UTRs)
   Position: mm10 chr10:42,561,963-42,583,632 Size: 21,670 Total Exon Count: 9 Strand: -
Coding Region
   Position: mm10 chr10:42,563,364-42,582,906 Size: 19,543 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:42,561,963-42,583,632)mRNA (may differ from genome)Protein (385 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: Q78ZM1_MOUSE
DESCRIPTION: SubName: Full=Nuclear receptor 2E1; SubName: Full=Nuclear receptor subfamily 2, group E, member 1;
SIMILARITY: Belongs to the nuclear hormone receptor family.
SIMILARITY: Contains 1 nuclear receptor DNA-binding 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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -305.80726-0.421 Picture PostScript Text
3' UTR -346.901401-0.248 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
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on Q78ZM1
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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
No orthologGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
 RGDEnsemblEnsemblWormBase 
 Protein Sequence Protein SequenceProtein Sequence 
 Alignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0008270 zinc ion binding
GO:0019899 enzyme binding
GO:0042826 histone deacetylase binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001662 behavioral fear response
GO:0002118 aggressive behavior
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007420 brain development
GO:0007601 visual perception
GO:0008284 positive regulation of cell proliferation
GO:0008347 glial cell migration
GO:0021542 dentate gyrus development
GO:0021764 amygdala development
GO:0021772 olfactory bulb development
GO:0021819 layer formation in cerebral cortex
GO:0021872 forebrain generation of neurons
GO:0021895 cerebral cortex neuron differentiation
GO:0021960 anterior commissure morphogenesis
GO:0021987 cerebral cortex development
GO:0030198 extracellular matrix organization
GO:0035019 somatic stem cell population maintenance
GO:0035176 social behavior
GO:0043010 camera-type eye development
GO:0043066 negative regulation of apoptotic process
GO:0043401 steroid hormone mediated signaling pathway
GO:0045165 cell fate commitment
GO:0045665 negative regulation of neuron differentiation
GO:0045766 positive regulation of angiogenesis
GO:0045787 positive regulation of cell cycle
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048712 negative regulation of astrocyte differentiation
GO:0048814 regulation of dendrite morphogenesis
GO:0051128 regulation of cellular component organization
GO:0060041 retina development in camera-type eye
GO:0060164 regulation of timing of neuron differentiation
GO:0060291 long-term synaptic potentiation
GO:0090049 regulation of cell migration involved in sprouting angiogenesis
GO:2000178 negative regulation of neural precursor cell proliferation
GO:2000179 positive regulation of neural precursor cell proliferation
GO:2000648 positive regulation of stem cell proliferation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC057104 - Mus musculus nuclear receptor subfamily 2, group E, member 1, mRNA (cDNA clone MGC:63295 IMAGE:6401770), complete cds.
BC056950 - Mus musculus cDNA clone IMAGE:6811142, containing frame-shift errors.
AK132201 - Mus musculus 10 days embryo whole body cDNA, RIKEN full-length enriched library, clone:3425403H08 product:nuclear receptor subfamily 2, group E, member 1, full insert sequence.
S77482 - mtll=tailless homolog [mice, embryos, mRNA, 2026 nt].
AK135694 - Mus musculus in vitro fertilized eggs cDNA, RIKEN full-length enriched library, clone:7420404H10 product:nuclear receptor subfamily 2, group E, member 1, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: mCG_18797, NM_152229, Q78ZM1, Q78ZM1_MOUSE, uc007eyt.1, uc007eyt.2
UCSC ID: uc007eyt.2
RefSeq Accession: NM_152229
Protein: Q78ZM1 CCDS: CCDS23813.1

-  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.