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Neurod4 neurogenic differentiation 4 [ Mus musculus (house mouse) ]

Gene ID: 11923, updated on 4-Jan-2025

Summary

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Official Symbol
Neurod4provided by MGI
Official Full Name
neurogenic differentiation 4provided by MGI
Primary source
MGI:MGI:108055
See related
Ensembl:ENSMUSG00000048015 AllianceGenome:MGI:108055
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ATH-3; Atoh3; Math3; MATH-3; bHLHa4
Summary
This gene belongs to the neurogenic differentiation factor family and encodes a basic helix-loop-helix (bHLH) transcription factor which is expressed in the developing nervous system with high levels of expression in the brain, retina and cranial ganglions. Expression gradually becomes restricted to the neural retina. It is a key gene in the Ngn2-regulated neuronal differentiation pathway, coordinating the onset of cortical gene transcription. This gene also regulates amacrine cell fate determination in the retina. [provided by RefSeq, Jul 2016]
Expression
Biased expression in CNS E11.5 (RPKM 1.8), CNS E14 (RPKM 0.6) and 4 other tissues See more
Orthologs
human all
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Genomic context

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See Neurod4 in Genome Data Viewer
Location:
10 D3; 10 77.81 cM
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (130104021..130116123, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (130268152..130280254, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 9 subfamily K member 2B Neighboring gene olfactory receptor family 9 subfamily K member 7 Neighboring gene STARR-seq mESC enhancer starr_28331 Neighboring gene STARR-positive B cell enhancer ABC_E9814 Neighboring gene STARR-seq mESC enhancer starr_28332 Neighboring gene STARR-positive B cell enhancer mm9_chr10:129735744-129736044 Neighboring gene STARR-positive B cell enhancer ABC_E8379 Neighboring gene STARR-positive B cell enhancer ABC_E11762 Neighboring gene STARR-positive B cell enhancer mm9_chr10:129774366-129774667 Neighboring gene thymocyte expressed, positive selection associated 1 Neighboring gene STARR-positive B cell enhancer mm9_chr10:129800808-129801109 Neighboring gene STARR-seq mESC enhancer starr_28333 Neighboring gene vomeronasal 2, receptor 84

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Basic helix-loop-helix proteins expressed during early embryonic organogenesis. Hjalt T. Int Rev Cytol, 2004. PMID 15261740
  2. Structure and promoter analysis of Math3 gene, a mouse homolog of Drosophila proneural gene atonal. Neural-specific expression by dual promoter elements. Tsuda H, et al. J Biol Chem, 1998 Mar 13. PMID 9497361
  3. An overview of the basic helix-loop-helix proteins. Jones S. Genome Biol, 2004. PMID 15186484, Free PMC Article
  4. Extremely low-frequency electromagnetic fields affect transcript levels of neuronal differentiation-related genes in embryonic neural stem cells. Ma Q, et al. PLoS One, 2014. PMID 24595264, Free PMC Article
  5. Conversion of ectoderm into a neural fate by ATH-3, a vertebrate basic helix-loop-helix gene homologous to Drosophila proneural gene atonal. Takebayashi K, et al. EMBO J, 1997 Jan 15. PMID 9029157, Free PMC Article

See all (104) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The expression of miR-544a was significantly decreased after spinal cord injury. High expression of miR-544a could alleviate the inflammation caused by spinal cord injury and promote the recovery of spinal cord via the inhibition of NEUROD4.
    Title: miRNA-544a Regulates the Inflammation of Spinal Cord Injury by Inhibiting the Expression of NEUROD4.
  2. In the sensory ganglia, early expression of NeuroD4 is terminated in mid gestation by Brn3a and Isl1 which bind to a shared enhancer in the NeuroD4 locus.
    Title: Brn3a and Islet1 act epistatically to regulate the gene expression program of sensory differentiation.
  3. Neurod4 cooperates to specify a cortical projection neuron identity.
    Title: Basic helix-loop-helix transcription factors cooperate to specify a cortical projection neuron identity.
  4. Math3 are essential, but not sufficient, for amacrine cell genesis.
    Title: Math3 and NeuroD regulate amacrine cell fate specification in the retina.
  5. Mash1 and Math3 promote branchiomotor neuron development and also regulate subsequent oligodendrocyte development and cytoarchitecture by maintaining neural progenitors through Notch signaling.
    Title: Mash1 and Math3 are required for development of branchiomotor neurons and maintenance of neural progenitors.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables E-box binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within Notch signaling pathway IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in amacrine cell differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in axon development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in camera-type eye development IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within camera-type eye development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within cell fate commitment IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within motor neuron migration IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within motor neuron migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within neuroblast proliferation IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within neuron development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within oligodendrocyte differentiation IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of cell differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
neurogenic differentiation factor 4
Names
atonal homolog 3
helix-loop-helix protein mATH-3

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)

  1. NM_001329489.1 → NP_001316418.1  neurogenic differentiation factor 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AC152977, AI846749, CO432182
    Consensus CDS
    CCDS24353.1
    UniProtKB/Swiss-Prot
    O09105
    UniProtKB/TrEMBL
    Q545C0
    Conserved Domains (2) summary
    cd00083
    Location:88 → 144
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam12533
    Location:146 → 263
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor

  2. NM_001329490.1 → NP_001316419.1  neurogenic differentiation factor 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AC152977, AI846749, CK627641
    Consensus CDS
    CCDS24353.1
    UniProtKB/Swiss-Prot
    O09105
    UniProtKB/TrEMBL
    Q545C0
    Conserved Domains (2) summary
    cd00083
    Location:88 → 144
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam12533
    Location:146 → 263
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor

  3. NM_007501.5 → NP_031527.1  neurogenic differentiation factor 4

    See identical proteins and their annotated locations for NP_031527.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AI846749, BC054391, CN526913, CO431699
    Consensus CDS
    CCDS24353.1
    UniProtKB/Swiss-Prot
    O09105
    UniProtKB/TrEMBL
    Q545C0
    Related
    ENSMUSP00000051379.4, ENSMUST00000061571.5
    Conserved Domains (2) summary
    cd00083
    Location:88 → 144
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam12533
    Location:146 → 263
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    130104021..130116123 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O09105.1 GenPept UniProtKB/Swiss-Prot:O09105

Gene LinkOut

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