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    six6a SIX homeobox 6a [ Danio rerio (zebrafish) ]

    Gene ID: 394080, updated on 9-Dec-2024

    Summary

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    Official Symbol
    six6aprovided by ZNC
    Official Full Name
    SIX homeobox 6aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1282
    See related
    Ensembl:ENSDARG00000025187 AllianceGenome:ZFIN:ZDB-GENE-040426-1282
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    Six6; zgc:63871
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within gene expression and neural retina development. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including eye; heart; integument; kidney; and telencephalon. Human ortholog(s) of this gene implicated in optic disc anomalies with retinal and/or macular dystrophy. Orthologous to human SIX6 (SIX homeobox 6). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See six6a in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (31583034..31606247)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (31473538..31475797)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene dehydrogenase/reductase (SDR family) member 7 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent, 1Aa Neighboring gene SIX homeobox 1a Neighboring gene SIX homeobox 4a

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Discovery and functional annotation of SIX6 variants in primary open-angle glaucoma. Carnes MU, et al. PLoS Genet, 2014. PMID 24875647, Free PMC Article
    2. Exome sequencing and functional analyses suggest that SIX6 is a gene involved in an altered proliferation-differentiation balance early in life and optic nerve degeneration at old age. Iglesias AI, et al. Hum Mol Genet, 2014 Mar 1. PMID 24150847
    3. Transcriptome analysis of the zebrafish atoh7-/- Mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases. Covello G, et al. FASEB Bioadv, 2020 Jul. PMID 32676583, Free PMC Article
    4. The bHLH Transcription Factor NeuroD Governs Photoreceptor Genesis and Regeneration Through Delta-Notch Signaling. Taylor SM, et al. Invest Ophthalmol Vis Sci, 2015 Nov. PMID 26580854, Free PMC Article
    5. Molecular codes and in vitro generation of hypocretin and melanin concentrating hormone neurons. Seifinejad A, et al. Proc Natl Acad Sci U S A, 2019 Aug 20. PMID 31375626, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Six6b and six7 govern expression of the SWS2 and RH2 opsins responsible for middle-wavelength sensitivity.
      Title: Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Clone Names

    • MGC63871

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in eye development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within gene expression IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neural retina development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein SIX6a
    Names
    sine oculis homeobox homolog 6
    sine oculis-related homeobox 6a

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_201105.1 → NP_957399.1  homeobox protein SIX6a

      See identical proteins and their annotated locations for NP_957399.1

      Status: PROVISIONAL

      Source sequence(s)
      BC053123
      UniProtKB/TrEMBL
      A0A8M1PFL8, Q7T3G8
      Related
      ENSDARP00000030834.4, ENSDART00000030646.5
      Conserved Domains (2) summary
      cd00086
      Location:130 → 178
      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:9 → 122
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007124.7 Reference GRCz11 Primary Assembly

      Range
      31583034..31606247
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068212822.1 → XP_068068923.1  homeobox protein SIX6a isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

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