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    six9 SIX homeobox 9 [ Danio rerio (zebrafish) ]

    Gene ID: 30623, updated on 2-Nov-2024

    Summary

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    Official Symbol
    six9provided by ZNC
    Official Full Name
    SIX homeobox 9provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-990621-11
    See related
    Ensembl:ENSDARG00000068407 AllianceGenome:ZFIN:ZDB-GENE-990621-11
    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
    si:dkey-149j18.3
    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. Predicted to be involved in regulation of skeletal muscle cell proliferation; regulation of transcription by RNA polymerase II; and skeletal muscle fiber development. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See six9 in Genome Data Viewer
    Location:
    chromosome: 18
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 18 NC_007129.7 (37237662..37241318, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 18 NC_007129.6 (37256302..37262389, complement)

    Chromosome 18 - NC_007129.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137488320 Neighboring gene glutaminyl-peptide cyclotransferase-like a Neighboring gene SIX homeobox 5 Neighboring gene tubulin folding cofactor B

    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. Six class homeobox genes in drosophila belong to three distinct families and are involved in head development. Seo HC, et al. Mech Dev, 1999 May. PMID 10381573
    2. Phylogenetic and Expression Analysis of Fos Transcription Factors in Zebrafish. Kubra K, et al. Int J Mol Sci, 2022 Sep 3. PMID 36077499, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC194500

    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 DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    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
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of skeletal muscle cell proliferation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skeletal muscle fiber development 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
    SIX homeobox 9
    Names
    sine oculis homeobox homolog 9

    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_001130608.1 → NP_001124080.1  SIX homeobox 9

      See identical proteins and their annotated locations for NP_001124080.1

      Status: PROVISIONAL

      Source sequence(s)
      BC163024
      UniProtKB/TrEMBL
      A0A8M3AV20, B3DI74
      Related
      ENSDARP00000072527.3, ENSDART00000078064.5
      Conserved Domains (2) summary
      cd00086
      Location:133 → 184
      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:5 → 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_007129.7 Reference GRCz11 Primary Assembly

      Range
      37237662..37241318 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009293776.4 → XP_009292051.1  SIX homeobox 9 isoform X1

      See identical proteins and their annotated locations for XP_009292051.1

      UniProtKB/TrEMBL
      A0A8M3AV20, B3DI74
      Conserved Domains (2) summary
      cd00086
      Location:133 → 184
      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:5 → 122
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
    Nucleotide Protein Strain
    Heading Accession and Version

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