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    Six4 sine oculis-related homeobox 4 [ Mus musculus (house mouse) ]

    Gene ID: 20474, updated on 9-Dec-2024

    Summary

    Official Symbol
    Six4provided by MGI
    Official Full Name
    sine oculis-related homeobox 4provided by MGI
    Primary source
    MGI:MGI:106034
    See related
    Ensembl:ENSMUSG00000034460 AllianceGenome:MGI:106034
    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
    AREC3; TrexBF
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of morphogenesis of an epithelium; regulation of DNA-templated transcription; and striated muscle cell differentiation. Acts upstream of or within several processes, including embryonic organ morphogenesis; myoblast migration; and thymus development. Located in cytoplasm and nucleus. Is expressed in several structures, including exocrine gland; genitourinary system; nervous system; sensory organ; and tongue. Orthologous to human SIX4 (SIX homeobox 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in limb E14.5 (RPKM 2.1), CNS E11.5 (RPKM 1.4) and 15 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Six4 in Genome Data Viewer
    Location:
    12 C3; 12 30.36 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (73146383..73160201, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (73099609..73114031, complement)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene sine oculis-related homeobox 6 Neighboring gene STARR-seq mESC enhancer starr_32458 Neighboring gene microRNA 9718 Neighboring gene sine oculis-related homeobox 1 Neighboring gene STARR-seq mESC enhancer starr_32461 Neighboring gene STARR-seq mESC enhancer starr_32463 Neighboring gene menage a trois 1 Neighboring gene predicted gene, 23910 Neighboring gene STARR-positive B cell enhancer ABC_E4028 Neighboring gene nuclear transport factor 2 pseudogene

    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)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within anatomical structure development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within embryonic cranial skeleton morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within embryonic skeletal system morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in fungiform papilla morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in generation of neurons IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within inner ear morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in male gonad development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in male sex determination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in male sex differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in metanephric mesenchyme development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within myoblast migration IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in myotome development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of satellite cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in olfactory placode formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pharyngeal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of branching involved in ureteric bud morphogenesis 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 ureteric bud formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of branch elongation involved in ureteric bud branching IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within regulation of protein localization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within regulation of synaptic assembly at neuromuscular junction IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sarcomere organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal muscle fiber differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle tissue development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in skeletal muscle tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within thymus development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in tongue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in trigeminal ganglion development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IC
    Inferred by Curator
    more info
    PubMed 
    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 SIX4
    Names
    sine oculis-related homeobox 4 homolog
    skeletal muscle-specific ARE-binding protein AREC3

    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_001362272.2NP_001349201.1  homeobox protein SIX4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC159274
      Consensus CDS
      CCDS88351.1
      UniProtKB/TrEMBL
      H3BL91
      Related
      ENSMUSP00000135699.3, ENSMUST00000175693.3
      Conserved Domains (2) summary
      cd00086
      Location:213267
      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:93202
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
    2. NM_001409898.1NP_001396827.1  homeobox protein SIX4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC159274
    3. NM_011382.3NP_035512.1  homeobox protein SIX4 isoform 1

      See identical proteins and their annotated locations for NP_035512.1

      Status: VALIDATED

      Source sequence(s)
      AC159274
      Consensus CDS
      CCDS25974.1
      UniProtKB/Swiss-Prot
      B2RQH3, Q61321, Q61322, Q61323
      Related
      ENSMUSP00000036150.7, ENSMUST00000043208.8
      Conserved Domains (2) summary
      cd00086
      Location:221275
      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:101210
      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_000078.7 Reference GRCm39 C57BL/6J

      Range
      73146383..73160201 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)