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    sox5 SRY-box transcription factor 5 [ Danio rerio (zebrafish) ]

    Gene ID: 567413, updated on 9-Dec-2024

    Summary

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    Official Symbol
    sox5provided by ZNC
    Official Full Name
    SRY-box transcription factor 5provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000607-13
    See related
    Ensembl:ENSDARG00000011582 AllianceGenome:ZFIN:ZDB-GENE-000607-13
    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
    sb:eu456; id:ibd5067; si:dkey-215a8.1
    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 with a negative effect on iridophore differentiation; melanocyte differentiation; and xanthophore differentiation. Predicted to be active in nucleus. Is expressed in several structures, including brain; digestive system; fin; forebrain neural keel; and gonad. Orthologous to human SOX5 (SRY-box transcription factor 5). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See sox5 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 4 NC_007115.7 (16981414..17216212, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 4 NC_007115.6 (16992452..17255766, complement)

    Chromosome 4 - NC_007115.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137491538 Neighboring gene ethanolamine kinase 1 Neighboring gene uncharacterized LOC137491396 Neighboring gene uncharacterized LOC137491539 Neighboring gene dynein axonemal intermediate chain 7

    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. Molecular cloning, expression of Sox5 and its down-regulation of Dmrt1 transcription in zebrafish. Gao S, et al. J Exp Zool B Mol Dev Evol, 2005 Sep 15. PMID 15981199
    2. Distinct interactions of Sox5 and Sox10 in fate specification of pigment cells in medaka and zebrafish. Nagao Y, et al. PLoS Genet, 2018 Apr. PMID 29621239, Free PMC Article
    3. Enhancers reside in a unique epigenetic environment during early zebrafish development. Kaaij LJ, et al. Genome Biol, 2016 Jul 5. PMID 27381023, Free PMC Article
    4. WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome. Tian Y, et al. Nat Commun, 2022 Sep 16. PMID 36114168, Free PMC Article
    5. The role of Sox6 in zebrafish muscle fiber type specification. Jackson HE, et al. Skelet Muscle, 2015. PMID 25671076, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within_negative_effect iridophore differentiation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within_negative_effect melanocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within_negative_effect xanthophore differentiation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor SOX-5
    Names
    SRY (sex determining region Y)-box 5
    SRY-box containing gene 5
    sox5b

    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_001033585.1 → NP_001028757.1  transcription factor SOX-5

      See identical proteins and their annotated locations for NP_001028757.1

      Status: PROVISIONAL

      Source sequence(s)
      AY730586
      UniProtKB/TrEMBL
      Q3ZM07
      Related
      ENSDARP00000137633.2, ENSDART00000162945.2
      Conserved Domains (1) summary
      cd01388
      Location:557 → 628
      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 ...

    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_007115.7 Reference GRCz11 Primary Assembly

      Range
      16981414..17216212 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021475103.2 → XP_021330778.1  transcription factor SOX-5 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PUN3
      Conserved Domains (2) summary
      cd01388
      Location:557 → 628
      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 vertebrates, and ...
      cl27863
      Location:328 → 411
      SSL_OB; Staphylococcal superantigen-like OB-fold domain

    2. XM_068219720.1 → XP_068075821.1  transcription factor SOX-5 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PUN3

    3. XM_068219719.1 → XP_068075820.1  transcription factor SOX-5 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PUN3

    4. XM_068219718.1 → XP_068075819.1  transcription factor SOX-5 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PUN3

    5. XM_068219717.1 → XP_068075818.1  transcription factor SOX-5 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PUN3

    6. XM_005164766.5 → XP_005164823.1  transcription factor SOX-5 isoform X4

      UniProtKB/TrEMBL
      A0A8M2BC41
      Related
      ENSDARP00000113921.1, ENSDART00000134595.3
      Conserved Domains (1) summary
      cd01388
      Location:556 → 627
      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 ...

    7. XM_021475095.2 → XP_021330770.1  transcription factor SOX-5 isoform X2

      UniProtKB/TrEMBL
      A0A8M9QBE2
      Conserved Domains (2) summary
      cd01388
      Location:560 → 631
      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 vertebrates, and ...
      cl27863
      Location:331 → 414
      SSL_OB; Staphylococcal superantigen-like OB-fold domain

    8. XM_005164767.5 → XP_005164824.1  transcription factor SOX-5 isoform X6

      UniProtKB/TrEMBL
      A0A8M2BBY9
      Conserved Domains (1) summary
      cd01388
      Location:529 → 600
      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 ...

    9. XM_021475104.2 → XP_021330779.1  transcription factor SOX-5 isoform X5

      UniProtKB/TrEMBL
      A0A8M9Q0P1
      Conserved Domains (1) summary
      cd01388
      Location:533 → 604
      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 vertebrates, and ...

    10. XM_021475094.2 → XP_021330769.1  transcription factor SOX-5 isoform X1

      UniProtKB/TrEMBL
      A0A8M9Q0N4
      Conserved Domains (2) summary
      cd01388
      Location:561 → 632
      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 vertebrates, and ...
      cl27863
      Location:332 → 415
      SSL_OB; Staphylococcal superantigen-like OB-fold domain
    Nucleotide Protein Strain
    Heading Accession and Version

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