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    SIX3 SIX homeobox 3 [ Homo sapiens (human) ]

    Gene ID: 6496, updated on 10-Dec-2024

    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; AllianceGenome:HGNC:10889
    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
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SIX3 in Genome Data Viewer
    Location:
    2p21
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (44941702..44946071)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (44946967..44951332)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45168841..45173210)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15686 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45089860-45089961 Neighboring gene VISTA enhancer hs149 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:45153974-45154534 Neighboring gene long intergenic non-protein coding RNA 1833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164020-45164553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164554-45165086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45166505-45167006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45167007-45167506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45168275-45168801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45169884-45170608 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45172898-45173404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11435 Neighboring gene SIX3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45182266-45182972 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45199471-45200338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45202291-45203066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45203067-45203842 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45227219-45228192 Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45232925-45233468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45233469-45234012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45235286-45236059 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: C5680330 GeneReviews: Not available
    not available
    Holoprosencephaly 2
    MedGen: C1834877 OMIM: 157170 GeneReviews: Holoprosencephaly Overview
    not available
    Schizencephaly
    MedGen: C0266484 OMIM: 269160 GeneReviews: Not available
    not available

    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

    EBI GWAS Catalog

    Description
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    EBI GWAS Catalog
    Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.
    EBI GWAS Catalog
    Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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
     
    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 DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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
     
    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
     
    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 homeobox-like protein 3

    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
      D6W5A5, O95343, Q53T42
      UniProtKB/TrEMBL
      A0A127AXB2
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      44946967..44951332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)