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Sall3 spalt like transcription factor 3 [ Mus musculus (house mouse) ]

Gene ID: 20689, updated on 29-Apr-2026
Official Symbol
Sall3provided by MGI
Official Full Name
spalt like transcription factor 3provided by MGI
Primary source
MGI:MGI:109295
See related
Ensembl:ENSMUSG00000024565 AllianceGenome:MGI:109295
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Sal; Msal; Salt; Spalt; Msal-1; B130022O04Rik
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within limb morphogenesis; negative regulation of smoothened signaling pathway; and olfactory bulb interneuron development. Predicted to be active in nucleus. Is expressed in several structures, including branchial arch; central nervous system; embryo mesenchyme; jaw; and sensory organ. Orthologous to human SALL3 (spalt like transcription factor 3). [provided by Alliance of Genome Resources, Jul 2025]
Expression
Biased expression in whole brain E14.5 (RPKM 3.6), frontal lobe adult (RPKM 3.4) and 7 other tissues See more
Orthologs
all
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Try the new Transcripts and proteins table
See Sall3 in Genome Data Viewer
Location:
18 E3; 18 54.11 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (81010204..81030236, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (80966989..80987021, complement)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 1 Neighboring gene predicted gene, 52342 Neighboring gene STARR-positive B cell enhancer mm9_chr18:80888627-80888928 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:80935003-80935320 Neighboring gene ATPase, class II, type 9B Neighboring gene STARR-seq mESC enhancer starr_45180 Neighboring gene STARR-positive B cell enhancer ABC_E7617 Neighboring gene STARR-seq mESC enhancer starr_45183 Neighboring gene predicted gene 27239 Neighboring gene ribosomal protein S8 pseudogene

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Related articles in PubMed

  1. The mouse homolog of the region specific homeotic gene spalt of Drosophila is expressed in the developing nervous system and in mesoderm-derived structures. Ott T, et al. Mech Dev, 1996 May. PMID 8798152
  2. The Sall3 locus is an epigenetic hotspot of aberrant DNA methylation associated with placentomegaly of cloned mice. Ohgane J, et al. Genes Cells, 2004 Mar. PMID 15005712
  3. Sall3 plays essential roles in horizontal cell maturation through regulation of neurofilament expression levels. Baba Y, et al. Biochimie, 2011 Jun. PMID 21396426
  4. A new member of the spalt like zinc finger protein family, Msal-3, is expressed in the CNS and sites of epithelial/mesenchymal interaction. Ott T, et al. Mech Dev, 2001 Mar. PMID 11231076
  5. Sall3 correlates with the expression of TH in mouse olfactory bulb. Heng X, et al. J Mol Neurosci, 2012 Feb. PMID 21701790

See all (73) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. show that the differentiation of group 3 ILCs is controlled by the glutamylation of IL-7Ralpha and the induction of transcription factor Sall3
    Title: IL-7Rα glutamylation and activation of transcription factor Sall3 promote group 3 ILC development.
  2. Sall3 & TH co-localize in olfactory bulb glomerular layer. Sall3 induces proximal TH promoter transcription. Sall3 deficiency causes reduction of TH expression.
    Title: Sall3 correlates with the expression of TH in mouse olfactory bulb.
  3. Sall3 plays essential roles in horizontal cell maturation through regulation of neurofilament expression levels
    Title: Sall3 plays essential roles in horizontal cell maturation through regulation of neurofilament expression levels.
  4. Our findings demonstrate that Sall3 plays a crucial role in regulating the development of both cone photoreceptors and horizontal interneurons. Lhx1 is one of the most strongly downregulated genes in Sall3 knockout mouse retinas.
    Title: The Spalt family transcription factor Sall3 regulates the development of cone photoreceptors and retinal horizontal interneurons.
  5. the antagonistic interaction between Hoxa13-Hoxd13 and Sall1-Sall3 in the developing limb may contribute to the fine-tuning of local Hox activity that leads to proper morphogenesis of each cartilage element of the vertebrate autopod.
    Title: Sall genes regulate region-specific morphogenesis in the mouse limb by modulating Hox activities.
  6. Sall3 is required for the terminal maturation of neurons destined for the glomerular layer.
    Title: Sall3 is required for the terminal maturation of olfactory glomerular interneurons.
  7. The Sall3 locus has aberrant DNA methylation associated with abnormal placental development of cloned mice.
    Title: The Sall3 locus is an epigenetic hotspot of aberrant DNA methylation associated with placentomegaly of cloned mice.
  8. Data suggest that Sall3 is required for the development of nerves that are derived from the hindbrain and for the formation of adjacent branchial arch derivatives.
    Title: Loss of the Sall3 gene leads to palate deficiency, abnormalities in cranial nerves, and perinatal lethality.
Submit: New GeneRIF Correction

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (3)  1 citation
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within forelimb morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within hindlimb morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of smoothened signaling pathway IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within olfactory bulb interneuron development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in olfactory bulb interneuron differentiation IEA
Inferred from Electronic Annotation
more info
  
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
  
Preferred Names
sal-like protein 3
Names
sal-like 3
spalt-like protein 3

NEW Try the new Transcript table

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_001369133.1 → NP_001356062.1  sal-like protein 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC125210
    Consensus CDS
    CCDS89289.1
    UniProtKB/Swiss-Prot
    Q08EB0, Q52KR5, Q62255, Q6GQT8, Q8BRD9
    UniProtKB/TrEMBL
    A0A5F8MPC9
    Related
    ENSMUSP00000158909.2, ENSMUST00000238808.2
    Conserved Domains (5) summary
    PHA03247
    Location:242 → 384
    PHA03247; large tegument protein UL36; Provisional
    COG5048
    Location:718 → 1168
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:694 → 714
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:1163 → 1183
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:706 → 731
    zf-H2C2_2; Zinc-finger double domain

  2. NM_178280.4 → NP_840064.2  sal-like protein 3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC125210, BC072631
    Consensus CDS
    CCDS29371.1
    UniProtKB/Swiss-Prot
    Q08EB0, Q52KR5, Q62255, Q6GQT8, Q8BRD9
    Related
    ENSMUSP00000056967.8, ENSMUST00000057950.9
    Conserved Domains (5) summary
    smart00355
    Location:427 → 449
    ZnF_C2H2; zinc finger
    COG5048
    Location:419 → 727
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:694 → 714
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:1091 → 1111
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:706 → 731
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    81010204..81030236 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030250368.2 → XP_030106228.1  sal-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q08EB0, Q52KR5, Q62255, Q6GQT8, Q8BRD9
    Conserved Domains (5) summary
    PHA03247
    Location:110 → 252
    PHA03247; large tegument protein UL36; Provisional
    COG5048
    Location:586 → 1036
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:562 → 582
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:1031 → 1051
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:574 → 599
    zf-H2C2_2; Zinc-finger double domain

  2. XM_036161040.1 → XP_036016933.1  sal-like protein 3 isoform X2

    UniProtKB/Swiss-Prot
    Q08EB0, Q52KR5, Q62255, Q6GQT8, Q8BRD9
    Conserved Domains (6) summary
    PHA03247
    Location:110 → 252
    PHA03247; large tegument protein UL36; Provisional
    COG5048
    Location:287 → 595
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:562 → 582
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:620 → 642
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:574 → 599
    zf-H2C2_2; Zinc-finger double domain
    cd20908
    Location:294 → 376
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q62255.2 GenPept UniProtKB/Swiss-Prot:Q62255

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