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    Six3 sine oculis-related homeobox 3 [ Mus musculus (house mouse) ]

    Gene ID: 20473, updated on 9-Dec-2024

    Summary

    Official Symbol
    Six3provided by MGI
    Official Full Name
    sine oculis-related homeobox 3provided by MGI
    Primary source
    MGI:MGI:102764
    See related
    Ensembl:ENSMUSG00000038805 AllianceGenome:MGI:102764
    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
    Six3a; Six3b; Six3beta; Six3alpha; E130112M24Rik
    Summary
    Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; histone deacetylase binding activity; and transcription corepressor binding activity. Involved in several processes, including camera-type eye development; forebrain development; and regulation of DNA-templated transcription. Acts upstream of or within several processes, including forebrain development; lens induction in camera-type eye; and protein import into nucleus. Located in nucleus. Is expressed in several structures, including alimentary system; embryo ectoderm; limb; nervous system; and sensory organ. Used to study holoprosencephaly 2. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 2. Orthologous to human SIX3 (SIX homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in whole brain E14.5 (RPKM 5.7), CNS E14 (RPKM 5.3) and 2 other tissues See more
    Orthologs
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    Genomic context

    See Six3 in Genome Data Viewer
    Location:
    17 E4; 17 55.42 cM
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (85921036..85933619)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (85613608..85626191)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_43471 Neighboring gene ribosomal protein L31, pseudogene 16 Neighboring gene STARR-seq mESC enhancer starr_43472 Neighboring gene STARR-seq mESC enhancer starr_43473 Neighboring gene developmentally regulated GTP binding protein 2 pseudogene Neighboring gene SIX homeobox 3, opposite strand 1 Neighboring gene sine oculis-related homeobox 2 Neighboring gene Riken cDNA CJ186046 gene

    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)
    • Endonuclease-mediated (1) 
    • Targeted (8)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription corepressor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in apoptotic process involved in development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within camera-type eye development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in cell proliferation in forebrain IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within circadian behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within diencephalon development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in epithelial cell maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in eye development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within eye development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in eye development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within forebrain anterior/posterior pattern specification IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within forebrain anterior/posterior pattern specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in forebrain dorsal/ventral pattern formation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in forebrain dorsal/ventral pattern formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within gonad development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in lens development in camera-type eye IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lens fiber cell apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lens fiber cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within lens induction in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism growth IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of neuron differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neuroblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuroblast migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in optic vesicle morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within pituitary gland development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in pituitary gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within protein import into nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in proximal/distal axis specification IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell cycle phase transition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of neural precursor cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of neural retina development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within telencephalon development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in telencephalon development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in telencephalon regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within thyroid gland development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    homeobox protein SIX3
    Names
    sine oculis homeobox homolog 3
    sine oculis-related homeobox 3 homolog

    NCBI Reference Sequences (RefSeq)

    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)

    1. NM_011381.4NP_035511.2  homeobox protein SIX3

      See identical proteins and their annotated locations for NP_035511.2

      Status: VALIDATED

      Source sequence(s)
      AC166821, BC098096, CD351258
      Consensus CDS
      CCDS50203.1
      UniProtKB/Swiss-Prot
      P70176, P70177, Q4QQQ3, Q62233
      UniProtKB/TrEMBL
      Q52KB8
      Related
      ENSMUSP00000135312.3, ENSMUST00000176081.3
      Conserved Domains (2) summary
      cd00086
      Location:209257
      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.
      pfam16878
      Location:88201
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      85921036..85933619
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017317367.2XP_017172856.1  homeobox protein SIX3 isoform X1

      UniProtKB/TrEMBL
      Q52KB8
      Conserved Domains (2) summary
      cd00086
      Location:230278
      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.
      pfam16878
      Location:109222
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain