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

Gene ID: 567413, updated on 17-Sep-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 central nervous system; digestive system; fin; forebrain neural keel; and gonad. Orthologous to human SOX5 (SRY-box transcription factor 5). [provided by Alliance of Genome Resources, Apr 2022]
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 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 (26) 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
  
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 cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
involved_in positive regulation of chondrocyte differentiation 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
  
acts_upstream_of_or_within_negative_effect xanthophore differentiation IGI
Inferred from Genetic Interaction
more info
 PubMed 
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-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

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

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

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

  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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