Barx1 BarH-like homeobox 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Barx1provided by MGI
Official Full Name: BarH-like homeobox 1provided by MGI
Primary source: MGI:MGI:103124
See related: Ensembl:ENSMUSG00000021381 AllianceGenome:MGI:103124
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including endothelial cell differentiation; negative regulation of Wnt signaling pathway; and spleen development. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; branchial arch; central nervous system; limb; and sensory organ. Orthologous to human BARX1 (BARX homeobox 1). [provided by Alliance of Genome Resources, Jul 2025]
Expression: Biased expression in stomach adult (RPKM 96.9) and CNS E11.5 (RPKM 5.6) See more
Orthologs: all
: Try the new Gene page
Try the new Transcripts and proteins table

Genomic context

Location:: 13 A5; 13 24.9 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (48816512..48819983)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (48663036..48666507)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

BARX1 functions in intestinal rotation and stomach myogenesis occur through this small group of intermediary transcription factors.
Title: Control of stomach smooth muscle development and intestinal rotation by transcription factor BARX1.
Barx1 control of thoracic foregut specification and tracheo-esophageal septation is tightly associated with down-regulation of adjacent Wnt pathway activity
Title: Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation.
miR-7a and miR-203 control expression of the stomach homeotic regulator Barx1.
Title: Regulation of mouse stomach development and Barx1 expression by specific microRNAs.
Hoxa2 also repressed the expression of its downstream targets Barx1 within the palate.
Title: Hoxa2 plays a direct role in murine palate development.
Results describe the independent functions and mechanisms for homeobox gene Barx1 in patterning mouse stomach and spleen.
Title: Independent functions and mechanisms for homeobox gene Barx1 in patterning mouse stomach and spleen.
Data show that Barx1 antagonizes Wnt signaling, and Barx1 loss in the mesenchyme prevents stomach epithelial differentiation of overlying endoderm and induces intestine-specific genes instead.
Title: The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling.

Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (3)
Targeted (1) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

Barx1 (e-PCR), detects polymorphism
- UniSTS:526987

Barx1 (e-PCR), detects polymorphism
- UniSTS:526988

NoName (e-PCR)
- UniSTS:491210

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 DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within animal organ development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell-cell signaling	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell-cell signaling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithelial cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spleen development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within tissue development	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	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: homeobox protein BarH-like 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.