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    SIX2 SIX homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 10736, updated on 18-Sep-2024

    Summary

    Official Symbol
    SIX2provided by HGNC
    Official Full Name
    SIX homeobox 2provided by HGNC
    Primary source
    HGNC:HGNC:10888
    See related
    Ensembl:ENSG00000170577 MIM:604994; AllianceGenome:HGNC:10888
    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
    Summary
    This gene is a member of the vertebrate gene family which encode proteins homologous to the Drosophila 'sine oculis' homeobox protein. The encoded protein is a transcription factor which, like other members of this gene family, may be involved in limb or eye development. [provided by RefSeq, Dec 2008]
    Expression
    Biased expression in salivary gland (RPKM 4.1), prostate (RPKM 2.7) and 4 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See SIX2 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 (45005182..45009452, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (45010408..45014884, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45232321..45236591, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes 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 ATAC-STARR-seq lymphoblastoid silent region 11436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45182266-45182972 Neighboring gene SIX3 antisense RNA 1 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 SIX homeobox 3 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45227219-45228192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45233469-45234012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45232925-45233468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45235286-45236059 Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45237064-45237663 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45239927-45240747 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45261729-45262230 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:45266703-45267902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45291852-45292470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45298897-45299398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45299399-45299898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45303064-45303728 Neighboring gene uncharacterized LOC107985809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45396231-45396731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45397597-45398226 Neighboring gene long intergenic non-protein coding RNA 1121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45417644-45418148 Neighboring gene uncharacterized LOC105374576

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    EBI GWAS Catalog

    Description
    Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
    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

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in anterior/posterior axis specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in condensed mesenchymal cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic cranial skeleton morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digestive tract morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in kidney development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in kidney development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal cell differentiation involved in kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal stem cell maintenance involved in nephron morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal stem cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesodermal cell fate specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in middle ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nephron development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nephron morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of chondrocyte proliferation 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 protein import into nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of ossification 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
     
    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 SIX2
    Names
    sine oculis homeobox homolog 2

    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_009360.1 RefSeqGene

      Range
      4952..9222
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_016932.5NP_058628.3  homeobox protein SIX2

      See identical proteins and their annotated locations for NP_058628.3

      Status: REVIEWED

      Source sequence(s)
      AC012354, AF332197, AI299144, AI697804, BC024033
      Consensus CDS
      CCDS1822.1
      UniProtKB/Swiss-Prot
      Q9BXH7, Q9NPC8
      UniProtKB/TrEMBL
      Q8TBA2
      Related
      ENSP00000304502.6, ENST00000303077.7
      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_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
      45005182..45009452 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005264100.4XP_005264157.1  homeobox protein SIX2 isoform X1

      See identical proteins and their annotated locations for XP_005264157.1

      UniProtKB/TrEMBL
      Q8TBA2
      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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      45010408..45014884 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340217.1XP_054196192.1  homeobox protein SIX2 isoform X1

      UniProtKB/TrEMBL
      Q8TBA2