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    sall3a spalt-like transcription factor 3a [ Danio rerio (zebrafish) ]

    Gene ID: 560775, updated on 9-Dec-2024

    Summary

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    Official Symbol
    sall3aprovided by ZNC
    Official Full Name
    spalt-like transcription factor 3aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-020228-4
    See related
    Ensembl:ENSDARG00000079613 AllianceGenome:ZFIN:ZDB-GENE-020228-4
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    spa3; sall3
    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 transcription by RNA polymerase II. Predicted to be active in nucleus. Is expressed in central nervous system; motor neurons; and neural tube. Orthologous to human SALL3 (spalt like transcription factor 3). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See sall3a in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (6634253..6654587)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (6693595..6713911)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene membrane bound O-acyltransferase domain containing 1 Neighboring gene si:ch211-36i19.1 Neighboring gene uncharacterized LOC137487873 Neighboring gene zinc finger protein 407 Neighboring gene zinc finger protein 236

    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. Expression of three spalt (sal) gene homologues in zebrafish embryos. Camp E, et al. Dev Genes Evol, 2003 Feb. PMID 12590351
    2. Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain. Kuil LE, et al. Dis Model Mech, 2019 Mar 8. PMID 30765415, Free PMC Article
    3. Colony-Stimulating Factor 1 Receptor (CSF1R) Regulates Microglia Density and Distribution, but Not Microglia Differentiation In Vivo. Oosterhof N, et al. Cell Rep, 2018 Jul 31. PMID 30067976
    4. Yolk sac-derived Pdcd11-positive cells modulate zebrafish microglia differentiation through the NF-κB-Tgfβ1 pathway. Yang R, et al. Cell Death Differ, 2021 Jan. PMID 32709934, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (7) 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 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
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    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
    		  

    General protein information

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    Preferred Names
    sal-like protein 3
    Names
    sal-like 3
    sal-like 3a

    NCBI Reference Sequences (RefSeq)

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    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_007127.7 Reference GRCz11 Primary Assembly

      Range
      6634253..6654587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068214080.1 → XP_068070181.1  sal-like protein 3 isoform X1

    2. XM_005157847.5 → XP_005157904.1  sal-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M9PNL7, F1R6E0
      Related
      ENSDARP00000104082.2, ENSDART00000109276.4
      Conserved Domains (5) summary
      PHA03169
      Location:29 → 190
      PHA03169; hypothetical protein; Provisional
      COG5048
      Location:461 → 787
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:754 → 774
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:1165 → 1185
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:766 → 791
      zf-H2C2_2; Zinc-finger double domain

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394951.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      322773..343107
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068218799.1 → XP_068074900.1  sal-like protein 3 isoform X1

    2. XM_021472948.2 → XP_021328623.1  sal-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M9PNL7, F1R6E0
      Conserved Domains (5) summary
      PHA03169
      Location:29 → 190
      PHA03169; hypothetical protein; Provisional
      COG5048
      Location:461 → 787
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:754 → 774
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:1165 → 1185
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:766 → 791
      zf-H2C2_2; Zinc-finger double domain
    Nucleotide Protein
    Heading Accession and Version

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