Hoxa1 homeobox A1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxa1provided by MGI
Official Full Name: homeobox A1provided by MGI
Primary source: MGI:MGI:96170
See related: Ensembl:ENSMUSG00000029844 AllianceGenome:MGI:96170
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: ERA1; Hox-1.6
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Acts upstream of or within several processes, including cellular response to ethanol; cellular response to retinoic acid; and nervous system development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including brain; embryo ectoderm; embryo mesenchyme; genitourinary system; and gut. Used to study Athabaskan brainstem dysgenesis syndrome. Human ortholog(s) of this gene implicated in Athabaskan brainstem dysgenesis syndrome and autistic disorder. Orthologous to human HOXA1 (homeobox A1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset 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:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (52132573..52135299, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (52155367..52160007, 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?

Overexpression of Homeobox A1 Relieves Ovalbumin-Induced Asthma in Mice and Is Associated with Blocking of the NF-kappaB Signaling Pathway.
Title: Overexpression of Homeobox A1 Relieves Ovalbumin-Induced Asthma in Mice and Is Associated with Blocking of the NF-κB Signaling Pathway.
Variations in the poly-histidine repeat motif of HOXA1 contribute to bicuspid aortic valve in mouse and zebrafish.
Title: Variations in the poly-histidine repeat motif of HOXA1 contribute to bicuspid aortic valve in mouse and zebrafish.
miR-18a-3p Encourages Apoptosis of Chondrocyte in Osteoarthritis via HOXA1 Pathway.
Title: miR-18a-3p Encourages Apoptosis of Chondrocyte in Osteoarthritis via HOXA1 Pathway.
A distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. Enhancer deletion significantly inhibited expression of RA-induced Hoxa1 and endoderm master control genes. Hoxa1 directly regulates downstream target genes expression and then orchestrates RA-induced early differentiation of ESCs.
Title: A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation.
we provide evidence that HOXA1 displays an unexpectedly long half-life and demonstrate that PRDM14 can reduce the stability and affect the transcriptional activity of HOXA1.
Title: PRDM14, a putative histone methyl-transferase, interacts with and decreases the stability and activity of the HOXA1 transcription factor.
Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions.This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins
Title: HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.
Hoxa1 and Hoxb1 are required for pharyngeal arch artery development.
Title: Hoxa1 and Hoxb1 are required for pharyngeal arch artery development.
Authors found evidence for a high degree of evolutionary conservation of many binding regions and downstream targets of Hoxa1 between mouse and zebrafish.
Title: Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis.
Data indicate that homeobox A1 (HOXA1) was a direct microRNA miR-30b target in esophageal cancer (EC) cells.
Title: miR-30b inhibits cancer cell growth, migration, and invasion by targeting homeobox A1 in esophageal cancer.
In presence of these inducing agents, lipid accumulation as well as expression of HoxA1, HoxA5, HoxC4 &HoxC8 markedly enhanced. Irrespective of presence or absence of T3, insulin down regulates HoxA10. T3 results in over expression of HoxA5, HoxC4 and HoxC8 genes, whereas insulin up regulates expression of only HoxC8
Title: Fat accumulation in differentiated brown adipocytes is linked with expression of Hox genes.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Variation

Go to the top of the page Help

Alleles

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

Targeted (13) 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

UniSTS:143360 (e-PCR)
- UniSTS:143360

Hoxa1 (e-PCR), detects polymorphism
- UniSTS:143360

M22115 (e-PCR)
- UniSTS:124934

ha2793 (e-PCR)
- UniSTS:515597

NoName (e-PCR)
- UniSTS:484890

Hoxa1 (e-PCR), detects polymorphism
- UniSTS:470556

M22115 (e-PCR)
- UniSTS:163386

Hoxa1 (e-PCR), detects polymorphism
- UniSTS:536636

RH94642 (e-PCR)
- UniSTS:119889

NoName (e-PCR)
- UniSTS:495489

REN100302 (e-PCR)
- UniSTS:425099

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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 identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in abducens nerve formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anatomical structure morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in anatomical structure morphogenesis	ISO Inferred from Sequence Orthology 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 artery development	ISO Inferred from Sequence Orthology more info
involved_in artery morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cellular response to retinoic acid	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within central nervous system neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cochlea development	ISO Inferred from Sequence Orthology more info
involved_in cochlea morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cognition	ISO Inferred from Sequence Orthology more info
involved_in embryonic neurocranium morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within facial nerve structural organization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within facial nucleus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inner ear development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within motor neuron axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuromuscular process	ISO Inferred from Sequence Orthology more info
involved_in optokinetic behavior	ISO Inferred from Sequence Orthology more info
involved_in outer ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of behavior	ISO Inferred from Sequence Orthology 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 regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within rhombomere 3 development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within rhombomere 3 development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere 4 development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within rhombomere 4 development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere 5 development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within rhombomere 5 development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in semicircular canal formation	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: homeobox protein Hox-A1

Names: early retinoic acid 1; homeobox protein Hox-1.6; homeoboxless protein ERA-1-399; homeotic protein ERA-1-993

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.

mRNA and Protein(s)

NM_001311118.2 → NP_001298047.1 homeobox protein Hox-A1 isoform 2

Status: VALIDATED

Source sequence(s)

AC091106

Consensus CDS

CCDS80534.1

UniProtKB/TrEMBL

D3Z4E1

Related

ENSMUSP00000113724.2, ENSMUST00000120363.2
NM_010449.5 → NP_034579.3 homeobox protein Hox-A1 isoform 1

See identical proteins and their annotated locations for NP_034579.3

Status: VALIDATED

Source sequence(s)

AC091106

Consensus CDS

CCDS20138.1

UniProtKB/TrEMBL

B9EHK7, B9EHK8, Q8BNI8

Related

ENSMUSP00000000964.5, ENSMUST00000000964.6

Conserved Domains (2) summary

COG5576
Location:177 → 287

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:234 → 287

Homeobox; Homeobox domain