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

Gene ID: 560775, updated on 12-Sep-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, Apr 2022]
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 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
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