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

Gene ID: 20473, updated on 8-Feb-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 animal organ development; lens fiber cell apoptotic process; and neuroblast migration. Acts upstream of or within several processes, including animal organ development; circadian behavior; and protein import into nucleus. Located in nucleus. Is expressed in several structures, including embryo ectoderm; limb; maxillary process; 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, Apr 2022]
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)

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
 
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 development IEA
Inferred from Electronic Annotation
more info
 
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 
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)

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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_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