Hoxa6 homeobox A6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxa6provided by MGI
Official Full Name: homeobox A6provided by MGI
Primary source: MGI:MGI:96178
See related: Ensembl:ENSMUSG00000043219 AllianceGenome:MGI:96178
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
Also known as: Hox-1.2
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within anterior/posterior pattern specification and embryonic skeletal system development. Predicted to be located in nuclear speck. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; genitourinary system; gut; limb; and vertebral cartilage condensation. Orthologous to human HOXA6 (homeobox A6). [provided by Alliance of Genome Resources, Jun 2025]
Expression: Biased expression in colon adult (RPKM 5.1), ovary adult (RPKM 3.7) and 11 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 6 B3; 6 25.4 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (52181838..52185652, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (52204858..52208672, complement)

Chromosome 6 - NC_000072.7 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?

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)

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

Hoxa6 (e-PCR), detects polymorphism
- UniSTS:143370

Hoxa6 (e-PCR), detects polymorphism
- UniSTS:536644

UniSTS:467537 (e-PCR)
- UniSTS:467537

Hoxa6 (e-PCR), detects polymorphism
- UniSTS:467537

NoName (e-PCR)
- UniSTS:492898

Hoxa6 (e-PCR), detects polymorphism
- UniSTS:547735

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	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 cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic skeletal system development	IGI Inferred from Genetic Interaction 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

Component	Evidence Code	Pubs
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
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 Hox-A6

Names: homeo box A6; homeobox protein Hox-1.2; homeobox protein M5-4

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.