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    SIX3 SIX homeobox 3 [ Homo sapiens (human) ]

    Gene ID: 6496, updated on 15-Jun-2021

    Summary

    Official Symbol
    SIX3provided by HGNC
    Official Full Name
    SIX homeobox 3provided by HGNC
    Primary source
    HGNC:HGNC:10889
    See related
    Ensembl:ENSG00000138083 MIM:603714
    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
    HPE2
    Summary
    This gene encodes a member of the sine oculis homeobox transcription factor family. The encoded protein plays a role in eye development. Mutations in this gene have been associated with holoprosencephaly type 2. [provided by RefSeq, Oct 2009]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
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    Genomic context

    See SIX3 in Genome Data Viewer
    Location:
    2p21
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (44941702..44946071)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45168841..45173210)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs149 Neighboring gene long intergenic non-protein coding RNA 1833 Neighboring gene SIX3 antisense RNA 1 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene SIX homeobox 2

    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

    Associated conditions

    Description Tests
    Anophthalmia-microphthalmia syndrome
    MedGen: CN120488 GeneReviews: Not available
    Compare labs
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    GeneReviews: Not available
    Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.
    GeneReviews: Not available
    Holoprosencephaly 2
    MedGen: C1834877 OMIM: 157170 GeneReviews: Holoprosencephaly Overview
    Compare labs
    Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
    GeneReviews: Not available
    Schizencephaly
    MedGen: C0266484 OMIM: 269160 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-09-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-23)

    ClinGen Genome Curation PagePubMed

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • AC012354.6

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in apoptotic process involved in development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell proliferation in forebrain ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in epithelial cell maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in eye development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in eye development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in forebrain dorsal/ventral pattern formation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lens development in camera-type eye ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lens fiber cell apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lens fiber cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neuroblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuroblast migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in optic vesicle morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pituitary gland development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proximal/distal axis specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell cycle phase transition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of neural precursor cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of neural retina development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of neuroblast proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in telencephalon development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in telencephalon regionalization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in visual perception TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    homeobox protein SIX3
    Names
    sine oculis homeobox homolog 3
    sine oculis homeobox-like protein 3
    truncated SIX3

    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_016222.1 RefSeqGene

      Range
      4805..9174
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005413.4NP_005404.1  homeobox protein SIX3

      See identical proteins and their annotated locations for NP_005404.1

      Status: REVIEWED

      Source sequence(s)
      AC012354, AJ012611, BF570321, CD673488, EL952320
      Consensus CDS
      CCDS1821.1
      UniProtKB/Swiss-Prot
      O95343
      Related
      ENSP00000260653.3, ENST00000260653.5
      Conserved Domains (2) summary
      cd00086
      Location:208256
      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:87200
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      44941702..44946071
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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