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Hoxa1 homeobox A1 [ Mus musculus (house mouse) ]

Gene ID: 15394, updated on 15-Nov-2022

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, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See Hoxa1 in Genome Data Viewer
Location:
6 B3; 6 25.4 cM
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (52132347..52135297, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (52155367..52160007, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene Hoxa adjacent long noncoding RNA 1 Neighboring gene ribosomal protein S8, pseudogene 3 Neighboring gene Hoxa transcript antisense RNA, myeloid-specific 2 Neighboring gene Hoxa transcript antisense RNA, myeloid-specific 1 Neighboring gene homeobox A2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
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
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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 multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
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 DNA-templated transcription IEA
Inferred from Electronic Annotation
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
PubMed 
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
PubMed 

General protein information

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)

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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)

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

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses alternate splice sites in the 5' coding region, resulting in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK083575, AK143943
    Consensus CDS
    CCDS80534.1
    UniProtKB/TrEMBL
    D3Z4E1, Q8BNI8
    Related
    ENSMUSP00000113724.2, ENSMUST00000120363.2
  2. NM_010449.4NP_034579.3  homeobox protein Hox-A1 isoform 1

    See identical proteins and their annotated locations for NP_034579.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK083575, AK143943
    Consensus CDS
    CCDS20138.1
    UniProtKB/TrEMBL
    B9EHK7, Q8BNI8
    Related
    ENSMUSP00000000964.5, ENSMUST00000000964.6
    Conserved Domains (2) summary
    COG5576
    Location:177287
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:234287
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    52132347..52135297 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)