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    sox21b SRY-box transcription factor 21b [ Danio rerio (zebrafish) ]

    Gene ID: 406246, updated on 2-Nov-2024

    Summary

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    Official Symbol
    sox21bprovided by ZNC
    Official Full Name
    SRY-box transcription factor 21bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040429-1
    See related
    Ensembl:ENSDARG00000008540 AllianceGenome:ZFIN:ZDB-GENE-040429-1
    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
    zgc:110678
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within lens development in camera-type eye. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; otic vesicle; sensory system; solid lens vesicle; and testis. Orthologous to human SOX21 (SRY-box transcription factor 21). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See sox21b in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (53276356..53277702)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (53736849..53738195)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC110440052 Neighboring gene uncharacterized LOC137496512 Neighboring gene uncharacterized LOC137496511 Neighboring gene dopachrome tautomerase Neighboring gene glypican 6b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Comparative analysis of duplicated sox21 genes in zebrafish. Lan X, et al. Dev Growth Differ, 2011 Apr. PMID 21492149
    2. Lens development depends on a pair of highly conserved Sox21 regulatory elements. Pauls S, et al. Dev Biol, 2012 May 1. PMID 22387845, Free PMC Article
    3. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Bogdanović O, et al. Nat Genet, 2016 Apr. PMID 26928226, Free PMC Article
    4. Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Hufton AL, et al. Genome Res, 2009 Nov. PMID 19704032, Free PMC Article
    5. Ectopic expression and knockdown of a zebrafish sox21 reveal its role as a transcriptional repressor in early development. Argenton F, et al. Mech Dev, 2004 Feb. PMID 15037315

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription activator 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
    		  
    enables sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within lens development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    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
    		  

    General protein information

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    Preferred Names
    transcription factor Sox-21-B
    Names
    SRY (sex determining region Y)-box 21b

    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_001009888.2 → NP_001009888.1  transcription factor Sox-21-B

      See identical proteins and their annotated locations for NP_001009888.1

      Status: PROVISIONAL

      Source sequence(s)
      BC095366
      UniProtKB/Swiss-Prot
      Q6RVD7
      Related
      ENSDARP00000023480.6, ENSDART00000003310.8
      Conserved Domains (2) summary
      cd01388
      Location:7 → 78
      SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
      pfam12336
      Location:77 → 95
      SOXp; SOX transcription factor

    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_007120.7 Reference GRCz11 Primary Assembly

      Range
      53276356..53277702
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6RVD7.1 GenPept UniProtKB/Swiss-Prot:Q6RVD7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.