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Hoxa1 homeobox A1 [ Mus musculus (house mouse) ]

Gene ID: 15394, updated on 24-Jul-2015
Official Symbol
Hoxa1provided by MGI
Official Full Name
homeobox A1provided by MGI
Primary source
MGI:MGI:96170
See related
Ensembl:ENSMUSG00000029844; Vega:OTTMUSG00000018885
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ERA1; Hox-1.6
Orthologs
See Hoxa1 in Epigenomics, MapViewer
Location:
6 B3; 6 25.4 cM
Exon count:
3
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 6 NC_000072.6 (52155367..52160410, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (52105366..52108316, complement)

Chromosome 6 - NC_000072.6Genomic Context describing neighboring genes Neighboring gene Hoxa adjacent long noncoding RNA 1 Neighboring gene ribosomal protein S8, pseudogene 3 Neighboring gene uncharacterized LOC105242658 Neighboring gene homeobox A2 Neighboring gene Hoxa cluster antisense RNA 2 Neighboring gene homeobox A3

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
abducens nerve formation ISO
Inferred from Sequence Orthology
more info
 
anatomical structure formation involved in morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
anatomical structure morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
anatomical structure morphogenesis ISO
Inferred from Sequence Orthology
more info
 
anterior/posterior pattern specification IGI
Inferred from Genetic Interaction
more info
PubMed 
anterior/posterior pattern specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
artery development ISO
Inferred from Sequence Orthology
more info
 
artery morphogenesis ISO
Inferred from Sequence Orthology
more info
 
cellular response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
central nervous system neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cochlea development ISO
Inferred from Sequence Orthology
more info
 
cochlea morphogenesis ISO
Inferred from Sequence Orthology
more info
 
cognition ISO
Inferred from Sequence Orthology
more info
 
embryonic neurocranium morphogenesis ISO
Inferred from Sequence Orthology
more info
 
facial nerve structural organization IGI
Inferred from Genetic Interaction
more info
PubMed 
facial nucleus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
hindbrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner ear development ISO
Inferred from Sequence Orthology
more info
 
inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
motor neuron axon guidance IGI
Inferred from Genetic Interaction
more info
PubMed 
multicellular organismal development IEA
Inferred from Electronic Annotation
more info
 
nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuromuscular process ISO
Inferred from Sequence Orthology
more info
 
optokinetic behavior ISO
Inferred from Sequence Orthology
more info
 
outer ear morphogenesis ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
regulation of behavior ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
rhombomere 3 development IGI
Inferred from Genetic Interaction
more info
PubMed 
rhombomere 3 development IMP
Inferred from Mutant Phenotype
more info
PubMed 
rhombomere 4 development IGI
Inferred from Genetic Interaction
more info
PubMed 
rhombomere 4 development IMP
Inferred from Mutant Phenotype
more info
PubMed 
rhombomere 5 development IGI
Inferred from Genetic Interaction
more info
PubMed 
rhombomere 5 development IMP
Inferred from Mutant Phenotype
more info
PubMed 
semicircular canal formation ISO
Inferred from Sequence Orthology
more info
 
sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IEA
Inferred from Electronic Annotation
more info
 
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

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
  2. NM_010449.4NP_034579.3  homeobox protein Hox-A1

    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
    UniProtKB/TrEMBL
    Q8BNI8
    Related
    ENSMUSP00000000964, OTTMUSP00000020428, ENSMUST00000000964, OTTMUST00000045418
    Conserved Domains (2) summary
    COG5576
    Location:177287
    COG5576; Homeodomain-containing transcription factor [Transcription]
    cd00086
    Location:234289
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 105

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000072.6 Reference GRCm38.p3 C57BL/6J

    Range
    52155367..52160410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006505607.1XP_006505670.1  

    See identical proteins and their annotated locations for XP_006505670.1

    UniProtKB/TrEMBL
    B9EHK7
    Conserved Domains (2) summary
    COG5576
    Location:177287
    COG5576; Homeodomain-containing transcription factor [Transcription]
    cd00086
    Location:234289
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  2. XM_006505608.1XP_006505671.1  

    UniProtKB/TrEMBL
    D3Z4E1

Alternate Mm_Celera

Genomic

  1. AC_000028.1 Alternate Mm_Celera

    Range
    52677008..52679958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)