Human Gene NEUROD4 (ENST00000242994.4_4) from GENCODE V47lift37
  Description: neuronal differentiation 4 (from RefSeq NM_021191.3)
Gencode Transcript: ENST00000242994.4_4
Gencode Gene: ENSG00000123307.4_7
Transcript (Including UTRs)
   Position: hg19 chr12:55,413,758-55,423,801 Size: 10,044 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr12:55,420,224-55,421,219 Size: 996 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:55,413,758-55,423,801)mRNA (may differ from genome)Protein (331 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NDF4_HUMAN
DESCRIPTION: RecName: Full=Neurogenic differentiation factor 4; Short=NeuroD4; AltName: Full=Class A basic helix-loop-helix protein 4; Short=bHLHa4; AltName: Full=Protein atonal homolog 3; Short=ATH-3; Short=Atoh3;
FUNCTION: Probably acts as a transcriptional activator. Mediates neuronal differentiation. Required for the regulation of amacrine cell fate specification in the retina (By similarity).
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein (By similarity).
SUBCELLULAR LOCATION: Nucleus (Potential).
PTM: Serine or threonine phosphorylation within the basic region may regulate neurogenic activity (By similarity).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) 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


-  MalaCards Disease Associations
  MalaCards Gene Search: NEUROD4
Diseases sorted by gene-association score: congenital stationary night blindness (1)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.89 RPKM in Pituitary
Total median expression: 8.22 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -130.00349-0.372 Picture PostScript Text
3' UTR -592.502582-0.229 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
IPR011598 - HLH_dom
IPR022575 - Neurogenic_DUF
IPR016637 - TF_bHLH_NeuroD

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF12533 - Neuronal helix-loop-helix transcription factor

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q9HD90
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0001764 neuron migration
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007219 Notch signaling pathway
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007405 neuroblast proliferation
GO:0010001 glial cell differentiation
GO:0030154 cell differentiation
GO:0035881 amacrine cell differentiation
GO:0043010 camera-type eye development
GO:0045165 cell fate commitment
GO:0045597 positive regulation of cell differentiation
GO:0048666 neuron development
GO:0060041 retina development in camera-type eye

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK314136 - Homo sapiens cDNA, FLJ94834, highly similar to Homo sapiens neurogenic differentiation 4 (NEUROD4), mRNA.
JD319947 - Sequence 300971 from Patent EP1572962.
JD361693 - Sequence 342717 from Patent EP1572962.
AB464631 - Synthetic construct DNA, clone: pF1KB9628, Homo sapiens NEUROD4 gene for neurogenic differentiation 4, without stop codon, in Flexi system.
BC040961 - Homo sapiens neurogenic differentiation 4, mRNA (cDNA clone MGC:48946 IMAGE:5490979), complete cds.
KJ903017 - Synthetic construct Homo sapiens clone ccsbBroadEn_12411 NEUROD4 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: ATH3, ATOH3, B2RAC9, BHLHA4, ENST00000242994.1, ENST00000242994.2, ENST00000242994.3, NDF4_HUMAN, NM_021191, Q9HD90, uc317ele.1, uc317ele.2
UCSC ID: ENST00000242994.4_4
RefSeq Accession: NM_021191.3
Protein: Q9HD90 (aka NDF4_HUMAN)

-  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.