Vax1 ventral anterior homeobox 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vax1provided by MGI
Official Full Name: ventral anterior homeobox 1provided by MGI
Primary source: MGI:MGI:1277163
See related: Ensembl:ENSMUSG00000006270 AllianceGenome:MGI:1277163
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
Summary: This gene encodes a member of the EMX homeobox protein family. The encoded protein functions as a transcription factor which is important in the development of anterior ventral forebrain and visual system. Disruption of this gene causes impairment in the developing forebrain, where the encoded protein is necessary for axon guidance and major tract formation. [provided by RefSeq, Dec 2015]
Expression: Biased expression in whole brain E14.5 (RPKM 3.3), CNS E14 (RPKM 2.6) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 19 D3; 19 54.61 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (59152912..59158829, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (59164480..59170397, complement)

Chromosome 19 - NC_000085.7 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 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 transcription factor VAX1 in VIP neurons of the suprachiasmatic nucleus impacts circadian rhythm generation, depressive-like behavior, and the reproductive axis in a sex-specific manner in mice.
Title: The transcription factor VAX1 in VIP neurons of the suprachiasmatic nucleus impacts circadian rhythm generation, depressive-like behavior, and the reproductive axis in a sex-specific manner in mice.
Visuomotor anomalies in achiasmatic mice expressing a transfer-defective Vax1 mutant.
Title: Visuomotor anomalies in achiasmatic mice expressing a transfer-defective Vax1 mutant.
The transcription factors SIX3 and VAX1 are required for suprachiasmatic nucleus circadian output and fertility in female mice.
Title: The transcription factors SIX3 and VAX1 are required for suprachiasmatic nucleus circadian output and fertility in female mice.
Kiss1 is differentially regulated in male and female mice by the homeodomain transcription factor VAX1.
Title: Kiss1 is differentially regulated in male and female mice by the homeodomain transcription factor VAX1.
Transcription Factor VAX1 Regulates the Regional Specification of the Subpallium Through Repressing Gsx2.
Title: Transcription Factor VAX1 Regulates the Regional Specification of the Subpallium Through Repressing Gsx2.
Stem cell regionalization during olfactory bulb neurogenesis depends on regulatory interactions between Vax1 and Pax6.
Title: Stem cell regionalization during olfactory bulb neurogenesis depends on regulatory interactions between Vax1 and Pax6.
The Homeodomain Transcription Factors Vax1 and Six6 Are Required for SCN Development and Function.
Title: The Homeodomain Transcription Factors Vax1 and Six6 Are Required for SCN Development and Function.
Heterozygous deletion of Otx2, Vax1, or Six3 is sufficient to produce subfertility. Review shows that that all 3 have reduced numbers of GnRH neurons and are subfertile. However, there is specificity to the subfertility by sex and by mechanisms of action.
Title: Haploinsufficiency of Homeodomain Proteins Six3, Vax1, and Otx2 Causes Subfertility in Mice via Distinct Mechanisms.
In immature GN11 cells, VAX1 and cFOS enhance GnRH expression, whereas VAX1 and cFOS have a repressive role in the mature GT1-7 cells.
Title: Transcriptional interaction between cFOS and the homeodomain-binding transcription factor VAX1 on the GnRH promoter controls Gnrh1 expression levels in a GnRH neuron maturation specific manner.
Despite significant associations between VAX1 and human forms of CLP, we find no evidence of a direct role for this transcription factor in development of this region in a mutant mouse model.
Title: Vax1 Plays an Indirect Role in the Etiology of Murine Cleft Palate.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Variation

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Alleles

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

Endonuclease-mediated (1) 1 citation
Targeted (5) 1 citation

General gene information

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Markers

D19Mgc6 (e-PCR)
- UniSTS:256837

D19Mit137 (e-PCR), detects polymorphism
- UniSTS:128352

NoName (e-PCR)
- UniSTS:485016

Vax1 (e-PCR), detects polymorphism
- UniSTS:527604

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within astrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of neuroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of neuroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuroepithelial cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within roof of mouth development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within skeletal muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ventral anterior homeobox 1

Names: ventral anterior homeobox containing gene 1

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_009501.3 → NP_033527.1 ventral anterior homeobox 1

See identical proteins and their annotated locations for NP_033527.1

Status: REVIEWED

Source sequence(s)

AC124459

Consensus CDS

CCDS29933.1

UniProtKB/Swiss-Prot

O88880, Q2NKI2

Related

ENSMUSP00000134642.2, ENSMUST00000172821.4

Conserved Domains (1) summary

pfam00046
Location:103 → 156

Homeobox; Homeobox domain

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

NC_000085.7 Reference GRCm39 C57BL/6J

Range

59152912..59158829 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006526916.2 → XP_006526979.1 ventral anterior homeobox 1 isoform X1

Conserved Domains (1) summary

pfam00046
Location:2 → 41

Homeobox; Homeobox domain