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    SIX1 SIX homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 6495, updated on 1-Jul-2024

    Summary

    Official Symbol
    SIX1provided by HGNC
    Official Full Name
    SIX homeobox 1provided by HGNC
    Primary source
    HGNC:HGNC:10887
    See related
    Ensembl:ENSG00000126778 MIM:601205; AllianceGenome:HGNC:10887
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BOS3; TIP39; DFNA23
    Summary
    The protein encoded by this gene is a homeobox protein that is similar to the Drosophila 'sine oculis' gene product. This gene is found in a cluster of related genes on chromosome 14 and is thought to be involved in limb development. Defects in this gene are a cause of autosomal dominant deafness type 23 (DFNA23) and branchiootic syndrome type 3 (BOS3). [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in salivary gland (RPKM 12.9), prostate (RPKM 9.2) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SIX1 in Genome Data Viewer
    Location:
    14q23.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60643421..60649477, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (54849879..54855949, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61110139..61116195, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ribosomal protein S15a pseudogene 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:61110622-61111184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61113614-61114236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61114237-61114858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61114859-61115480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61115481-61116101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5813 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61119031-61119800 Neighboring gene VISTA enhancer hs1602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5814 Neighboring gene senescence associated long non-coding RNA 1 Neighboring gene microRNA 9718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8481 Neighboring gene SIX homeobox 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8483 Neighboring gene MNAT1 component of CDK activating kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61246210-61246710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61246711-61247211 Neighboring gene mitotic arrest deficient 2 like 1 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-03-22)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-03-22)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma.
    EBI GWAS Catalog
    A genome-wide association study of optic disc parameters.
    EBI GWAS Catalog
    A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.
    EBI GWAS Catalog
    Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma.
    EBI GWAS Catalog
    Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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 activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 ISA
    Inferred from Sequence Alignment
    more info
     
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in aorta morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to 3,3',5-triiodo-L-thyronine IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cochlea morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic cranial skeleton morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in embryonic skeletal system morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in endothelin receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in facial nerve morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in fungiform papilla morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in generation of neurons ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal cell proliferation involved in ureter development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesonephric tubule formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric mesenchyme development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in middle ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myoblast migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in myoblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myotome development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural crest cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in olfactory placode formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in organ induction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in otic vesicle development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in outflow tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in pattern specification process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pharyngeal system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of brown fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of mesenchymal cell proliferation involved in ureter development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of myoblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of secondary heart field cardioblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in 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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of ureteric bud formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein localization to nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of branch elongation involved in ureteric bud branching ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of skeletal muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of skeletal muscle cell proliferation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of skeletal muscle satellite cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synaptic assembly at neuromuscular junction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skeletal muscle fiber development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal muscle tissue development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in thymus development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in thyroid gland development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in trigeminal ganglion development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ureter smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ureteric bud development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    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
     
    part_of transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    homeobox protein SIX1
    Names
    sine oculis homeobox homolog 1

    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.

    Genomic

    1. NG_008231.1 RefSeqGene

      Range
      4961..11017
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001425142.1NP_001412071.1  homeobox protein SIX1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL049874
    2. NM_005982.4NP_005973.1  homeobox protein SIX1 isoform 1

      See identical proteins and their annotated locations for NP_005973.1

      Status: REVIEWED

      Source sequence(s)
      AL049874, BC008874, X91868
      Consensus CDS
      CCDS9748.1
      UniProtKB/Swiss-Prot
      Q15475, Q53Y16, Q96H64
      Related
      ENSP00000494686.1, ENST00000645694.3
      Conserved Domains (2) summary
      cd00086
      Location:129180
      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:9118
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      60643421..60649477 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021602.3XP_016877091.1  homeobox protein SIX1 isoform X1

      Conserved Domains (2) summary
      pfam16878
      Location:9118
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
      cl00084
      Location:142167
      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.

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      54849879..54855949 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376625.1XP_054232600.1  homeobox protein SIX1 isoform X1