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

Gene ID: 11923, updated on 11-Apr-2024

Summary

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 differentiation IEA
Inferred from Electronic Annotation
more info
 
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 multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
 
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
 

General protein information

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_001329489.1NP_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:88144
    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:146263
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  2. NM_001329490.1NP_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:88144
    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:146263
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  3. NM_007501.5NP_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:88144
    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:146263
    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)