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    SIX4 SIX homeobox 4 [ Homo sapiens (human) ]

    Gene ID: 51804, updated on 9-Jun-2024

    Summary

    Official Symbol
    SIX4provided by HGNC
    Official Full Name
    SIX homeobox 4provided by HGNC
    Primary source
    HGNC:HGNC:10890
    See related
    Ensembl:ENSG00000100625 MIM:606342; AllianceGenome:HGNC:10890
    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
    AREC3
    Summary
    This gene encodes a member of the homeobox family, subfamily SIX. The drosophila homolog is a nuclear homeoprotein required for eye development. Studies in mouse show that this gene product functions as a transcription factor, and may have a role in the differentiation or maturation of neuronal cells. [provided by RefSeq, May 2010]
    Expression
    Broad expression in prostate (RPKM 2.0), salivary gland (RPKM 1.8) and 16 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SIX4 in Genome Data Viewer
    Location:
    14q23.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60709539..60724351, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (54916015..54930882, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61176257..61191069, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes 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 silent region 5814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8479 Neighboring gene senescence associated long non-coding RNA 1 Neighboring gene microRNA 9718 Neighboring gene SIX homeobox 1 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 8481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8480 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 OCT4-NANOG hESC enhancer GRCh37_chr14:61256800-61257329 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:61260034-61260243 Neighboring gene mitotic arrest deficient 2 like 1 pseudogene 1 Neighboring gene SRM pseudogene 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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-05-08)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-05-08)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC119450, MGC119452, MGC119453

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in embryonic cranial skeleton morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in fungiform papilla morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in generation of neurons ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in male gonad development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in male sex determination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in male sex differentiation 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 myoblast migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myotome development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of satellite cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in olfactory placode formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pharyngeal system development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of ureteric bud formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein localization to nucleus 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 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 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 sarcomere organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in skeletal muscle fiber differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in skeletal muscle tissue development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in thymus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tongue development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in trigeminal ganglion 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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    homeobox protein SIX4
    Names
    sine oculis homeobox homolog 4

    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_021182.1 RefSeqGene

      Range
      4784..19596
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017420.5NP_059116.3  homeobox protein SIX4

      See identical proteins and their annotated locations for NP_059116.3

      Status: REVIEWED

      Source sequence(s)
      AA424469, AL132777, BC099722
      Consensus CDS
      CCDS9749.2
      UniProtKB/Swiss-Prot
      Q4QQH5, Q4V764, Q9UIU6
      Related
      ENSP00000216513.4, ENST00000216513.5
      Conserved Domains (2) summary
      cd00086
      Location:228282
      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:108217
      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
      60709539..60724351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267759.3XP_005267816.1  homeobox protein SIX4 isoform X1

      Conserved Domains (2) summary
      cd00086
      Location:220274
      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:100209
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
    2. XM_047431474.1XP_047287430.1  homeobox protein SIX4 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      54916015..54930882 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376217.1XP_054232192.1  homeobox protein SIX4 isoform X1

    2. XM_054376218.1XP_054232193.1  homeobox protein SIX4 isoform X2