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    Pax6 paired box 6 [ Mus musculus (house mouse) ]

    Gene ID: 18508, updated on 29-Jun-2016
    Official Symbol
    Pax6provided by MGI
    Official Full Name
    paired box 6provided by MGI
    Primary source
    MGI:MGI:97490
    See related
    Ensembl:ENSMUSG00000027168 Vega:OTTMUSG00000015006
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Dey; Sey; AEY11; Pax-6; Gsfaey11; 1500038E17Rik
    Summary
    This gene encodes a homeobox-containing protein that functions as a regulator of transcription. It plays a key role in the development of neural tissues, particularly the eye. Activity of this protein is also required for expression of glucagon in the pancreas. This gene is regulated by multiple enhancers located up to tens or hundreds of kilobases upstream and downstream of the transcription start sites. Mutations in this gene or deletion of these regulatory elements results in severe defects in eye development. Alternative splicing and the use of alternative promoters results in multiple transcript variants, some of which encode proteins that lack the N-terminal paired domain. [provided by RefSeq, Jul 2015]
    Orthologs
    Location:
    2 E3; 2 55.31 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (105668896..105698410)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (105516602..105537226)

    Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene paired box 6 opposite strand 1 Neighboring gene predicted gene, 35946 Neighboring gene Pax6 upstream antisense RNA Neighboring gene elongator acetyltransferase complex subunit 4 Neighboring gene IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) Neighboring gene DnaJ heat shock protein family (Hsp40) member C24

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    AT DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    HMG box domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    R-SMAD binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    R-SMAD binding ISO
    Inferred from Sequence Orthology
    more info
     
    RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II core promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    RNA polymerase II transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II transcription factor activity, sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    co-SMAD binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    histone acetyltransferase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    anterior/posterior pattern specification IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    anterior/posterior pattern specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    astrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    astrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    blood vessel development ISO
    Inferred from Sequence Orthology
    more info
     
    brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    brain development ISO
    Inferred from Sequence Orthology
    more info
     
    camera-type eye development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    camera-type eye development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell fate commitment IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell fate determination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cerebral cortex regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    commitment of neuronal cell to specific neuron type in forebrain IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cornea development in camera-type eye ISO
    Inferred from Sequence Orthology
    more info
     
    dorsal/ventral axis specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic camera-type eye morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    epithelial cell development ISO
    Inferred from Sequence Orthology
    more info
     
    establishment of mitotic spindle orientation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    eye photoreceptor cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    forebrain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    forebrain dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    forebrain-midbrain boundary formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glucose homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    habenula development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    hindbrain development ISO
    Inferred from Sequence Orthology
    more info
     
    insulin metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    interkinetic nuclear migration ISO
    Inferred from Sequence Orthology
    more info
     
    iris morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    keratinocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lacrimal gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lens development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of neural precursor cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural crest cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    olfactory bulb development ISO
    Inferred from Sequence Orthology
    more info
     
    oligodendrocyte cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    pallium development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    pancreatic A cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    pancreatic A cell development ISO
    Inferred from Sequence Orthology
    more info
     
    pancreatic A cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    pituitary gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell fate specification ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of epithelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of glucagon secretion ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    protein localization to organelle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of asymmetric cell division IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of neurogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of neurogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of timing of cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription, DNA-templated TAS
    Traceable Author Statement
    more info
    PubMed 
    retina development in camera-type eye IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    rhombomere morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    salivary gland morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    signal transduction involved in regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    smoothened signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    telencephalon regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription from RNA polymerase II promoter ISO
    Inferred from Sequence Orthology
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    type B pancreatic cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    type B pancreatic cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    intracellular IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    transcription factor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    Preferred Names
    paired box protein Pax-6
    Names
    Dickie's small eye
    oculorhombin
    paired box gene 6

    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_001244198.2NP_001231127.1  paired box protein Pax-6 isoform 1

      See identical proteins and their annotated locations for NP_001231127.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). It initiates from the P0 promoter. Variants 1, 2, and 3 encode the same protein (isoform 1, also known as 5a).
      Source sequence(s)
      AK032616, AK139054, AL512589, CF724474, CN539723, CX565124
      Consensus CDS
      CCDS16499.1
      UniProtKB/Swiss-Prot
      P63015
      Related
      ENSMUSP00000106715, OTTMUSP00000015972, ENSMUST00000111086, OTTMUST00000035640
      Conserved Domains (2) summary
      cd00086
      Location:226283
      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.
      cd00131
      Location:5145
      PAX; Paired Box domain
    2. NM_001244200.2NP_001231129.1  paired box protein Pax-6 isoform 1

      See identical proteins and their annotated locations for NP_001231129.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. It initiates from the P1 promoter. Variants 1, 2, and 3 encode the same protein (isoform 1, also known as 5a).
      Source sequence(s)
      AK139054, AL512589, AY064175, CN538503, CN539723, CX565124
      Consensus CDS
      CCDS16499.1
      UniProtKB/Swiss-Prot
      P63015
      UniProtKB/TrEMBL
      Q8VBX9
      Related
      ENSMUSP00000129344, ENSMUST00000167211
      Conserved Domains (2) summary
      cd00086
      Location:226283
      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.
      cd00131
      Location:5145
      PAX; Paired Box domain
    3. NM_001244201.2NP_001231130.1  paired box protein Pax-6 isoform 2

      See identical proteins and their annotated locations for NP_001231130.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region compared to variant 1. It initiates from the P0 promoter. The encoded isoform (2) is shorter than isoform 1. Variants 4, 5, and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AK032616, AK139054, AL512589, CA751997, CN539723, CX565124
      Consensus CDS
      CCDS57181.1
      UniProtKB/Swiss-Prot
      P63015
      Related
      ENSMUSP00000106716, OTTMUSP00000015973, ENSMUST00000111087, OTTMUST00000035641
      Conserved Domains (3) summary
      cd00086
      Location:212269
      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.
      cd00131
      Location:5131
      PAX; Paired Box domain
      pfam13551
      Location:26128
      HTH_29; Winged helix-turn helix
    4. NM_001244202.2NP_001231131.1  paired box protein Pax-6 isoform 2

      See identical proteins and their annotated locations for NP_001231131.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 4, 5, and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AK045805, AK139054, AL512589, BF466986, CA751997, CN539723, CX565124
      Consensus CDS
      CCDS57181.1
      UniProtKB/Swiss-Prot
      P63015
      Related
      ENSMUSP00000106711, OTTMUSP00000015979, ENSMUST00000111082, OTTMUST00000035649
      Conserved Domains (3) summary
      cd00086
      Location:212269
      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.
      cd00131
      Location:5131
      PAX; Paired Box domain
      pfam13551
      Location:26128
      HTH_29; Winged helix-turn helix
    5. NM_001310144.1NP_001297073.1  paired box protein Pax-6 isoform 2

      See identical proteins and their annotated locations for NP_001297073.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an in-frame exon in the 5' coding region compared to variant 1. It initiates from the P1 promoter. The encoded isoform (2) is shorter than isoform 1. Variants 4, 5, and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AK139054, AL512589, AY064175, CD805985, CN539431, CN539723, CX565124
      Consensus CDS
      CCDS57181.1
      UniProtKB/Swiss-Prot
      P63015
      UniProtKB/TrEMBL
      Q8VBX9
      Related
      ENSMUSP00000087878, OTTMUSP00000015978, ENSMUST00000090397, OTTMUST00000035648
      Conserved Domains (3) summary
      cd00086
      Location:212269
      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.
      cd00131
      Location:5131
      PAX; Paired Box domain
      pfam13551
      Location:26128
      HTH_29; Winged helix-turn helix
    6. NM_001310145.1NP_001297074.1  paired box protein Pax-6 isoform 3

      See identical proteins and their annotated locations for NP_001297074.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and lacks a portion of the 5' coding region compared to variant 1. It initiates from the P alpha promoter. The encoded isoform (3) has a shorter N-terminus and lacks the paired domain, compared to isoform 1. Variants 7 and 8 encode the same protein (isoform 3, also known as DeltaPD).
      Source sequence(s)
      AK139054, AL512589, CK617741, CN539723, CX565124
      UniProtKB/Swiss-Prot
      P63015
      Conserved Domains (1) summary
      cd00086
      Location:76133
      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.
    7. NM_001310146.1NP_001297075.1  paired box protein Pax-6 isoform 3

      See identical proteins and their annotated locations for NP_001297075.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and lacks a portion of the 5' coding region compared to variant 1. It initiates from the P alpha promoter. The encoded isoform (3) has a shorter N-terminus and lacks the paired domain, compared to isoform 1. Variants 7 and 8 encode the same protein (isoform 3, also known as DeltaPD).
      Source sequence(s)
      AK139054, AL512589, CN539723, CV784112, CX565124
      UniProtKB/Swiss-Prot
      P63015
      Conserved Domains (1) summary
      cd00086
      Location:76133
      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.
    8. NM_013627.6NP_038655.1  paired box protein Pax-6 isoform 1

      See identical proteins and their annotated locations for NP_038655.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein (isoform 1, also known as 5a).
      Source sequence(s)
      AK045805, AK139054, AL512589, BF466986, CF724474, CN539723, CX565124
      Consensus CDS
      CCDS16499.1
      UniProtKB/Swiss-Prot
      P63015
      Related
      ENSMUSP00000087870, OTTMUSP00000015980, ENSMUST00000090391, OTTMUST00000035650
      Conserved Domains (2) summary
      cd00086
      Location:226283
      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.
      cd00131
      Location:5145
      PAX; Paired Box domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      105668896..105698410
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)