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

Gene ID: 394080, updated on 2-Nov-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, Nov 2024]
Orthologs
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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 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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