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

Gene ID: 20474, updated on 31-Jan-2019

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
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; AI047561
Expression
Broad expression in limb E14.5 (RPKM 2.1), CNS E11.5 (RPKM 1.4) and 15 other tissues See more
Orthologs

Genomic context

See Six4 in Genome Data Viewer
Location:
12; 12 C3
Exon count:
4
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 12 NC_000078.6 (73099609..73114770, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 12 NC_000078.5 (74201246..74214232, complement)

Chromosome 12 - NC_000078.6Genomic Context describing neighboring genes Neighboring gene sine oculis-related homeobox 6 Neighboring gene sine oculis-related homeobox 1 Neighboring gene menage a trois 1 Neighboring gene cytochrome c oxidase subunit 7A2, mitochondrial pseudogene Neighboring gene TRM5 tRNA methyltransferase 5

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 FunctionsWhat's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Process Evidence Code Pubs
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
anatomical structure development IGI
Inferred from Genetic Interaction
more info
PubMed 
embryonic cranial skeleton morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
embryonic skeletal system morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
fungiform papilla morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
generation of neurons IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner ear morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
male gonad development IMP
Inferred from Mutant Phenotype
more info
PubMed 
male sex determination IMP
Inferred from Mutant Phenotype
more info
PubMed 
male sex differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
metanephric mesenchyme development IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
myoblast migration IGI
Inferred from Genetic Interaction
more info
PubMed 
myotome development IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of neuron apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of satellite cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
olfactory placode formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
pharyngeal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of branching involved in ureteric bud morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of ureteric bud formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to nucleus IDA
Inferred from Direct Assay
more info
PubMed 
regulation of branch elongation involved in ureteric bud branching IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of protein localization IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of synaptic growth at neuromuscular junction IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
sarcomere organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
skeletal muscle fiber differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
skeletal muscle tissue development IGI
Inferred from Genetic Interaction
more info
PubMed 
skeletal muscle tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
thymus development IGI
Inferred from Genetic Interaction
more info
PubMed 
tongue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
trigeminal ganglion development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IC
Inferred by Curator
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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_001362272.1NP_001349201.1  homeobox protein SIX4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC159274, CJ180841, D50417
    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_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
    Q61321
    Related
    ENSMUSP00000036150.6, ENSMUST00000043208.7
    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: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000078.6 Reference GRCm38.p4 C57BL/6J

    Range
    73099609..73114770 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006515632.3XP_006515695.1  homeobox protein SIX4 isoform X1

    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
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