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    sall1a spalt-like transcription factor 1a [ Danio rerio (zebrafish) ]

    Gene ID: 555721, updated on 9-Dec-2024

    Summary

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    Official Symbol
    sall1aprovided by ZNC
    Official Full Name
    spalt-like transcription factor 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-020228-2
    See related
    Ensembl:ENSDARG00000074319 AllianceGenome:ZFIN:ZDB-GENE-020228-2
    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
    sall1; sb:eu809; cb896spalt; id:ibd5077
    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 embryonic pectoral fin morphogenesis and positive regulation of fibroblast growth factor receptor signaling pathway. Predicted to be active in nucleus. Is expressed in several structures, including fin; nervous system; neural keel; neural tube; and tail bud. Human ortholog(s) of this gene implicated in Townes-Brocks syndrome; middle lobe syndrome; and renal Wilms' tumor. Orthologous to human SALL1 (spalt like transcription factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See sall1a in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (37377335..37390778)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (37106077..37119520)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene TOX high mobility group box family member 3 Neighboring gene uncharacterized LOC137496100 Neighboring gene uncharacterized LOC137496101 Neighboring gene cylindromatosis (turban tumor syndrome)

    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. The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons. Bruckner JJ, et al. PLoS Biol, 2022 Nov. PMID 36318534, Free PMC Article
    3. sall4 acts downstream of tbx5 and is required for pectoral fin outgrowth. Harvey SA, et al. Development, 2006 Mar. PMID 16501170
    4. Functional and evolutionary insights from the Ciona notochord transcriptome. Reeves WM, et al. Development, 2017 Sep 15. PMID 28928284, Free PMC Article
    5. Transcriptional profiling of caudal fin regeneration in zebrafish. Schebesta M, et al. ScientificWorldJournal, 2006 Jun 2. PMID 17205186, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    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
    acts_upstream_of_or_within embryonic pectoral fin morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of fibroblast growth factor receptor signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    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 1a
    Names
    cb896
    sal-like 1a
    spa1a
    spalt1a

    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_001146014.1 → NP_001139486.1  sal-like protein 1a

      Status: PROVISIONAL

      Source sequence(s)
      CR388023
      UniProtKB/TrEMBL
      A0A8N7V0N8, F1QI36
      Related
      ENSDARP00000102655.3, ENSDART00000111842.5
      Conserved Domains (5) summary
      smart00355
      Location:443 → 465
      ZnF_C2H2; zinc finger
      sd00017
      Location:696 → 716
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:992 → 1012
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:1018 → 1040
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:708 → 733
      zf-H2C2_2; Zinc-finger double 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_007118.7 Reference GRCz11 Primary Assembly

      Range
      37377335..37390778
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021477534.2 → XP_021333209.1  sal-like protein 1a isoform X1

      UniProtKB/TrEMBL
      A0A1D5NSE4, A0A8M9Q7V5
      Related
      ENSDARP00000142758.1, ENSDART00000173652.2
      Conserved Domains (5) summary
      smart00355
      Location:347 → 369
      ZnF_C2H2; zinc finger
      sd00017
      Location:600 → 620
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:896 → 916
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:922 → 944
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:612 → 637
      zf-H2C2_2; Zinc-finger double domain

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394702.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      225309..238752
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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