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

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: human all
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Genomic context

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_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Neurod4 cooperates to specify a cortical projection neuron identity.
Title: Basic helix-loop-helix transcription factors cooperate to specify a cortical projection neuron identity.
Math3 are essential, but not sufficient, for amacrine cell genesis.
Title: Math3 and NeuroD regulate amacrine cell fate specification in the retina.
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)

Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI846749 (e-PCR)
- UniSTS:165731

Neurod4 (e-PCR), detects polymorphism
- UniSTS:507879

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)

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
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
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