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

    Gene ID: 20689, updated on 24-Dec-2024

    Summary

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    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 and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. 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, Dec 2024]
    Expression
    Biased expression in whole brain E14.5 (RPKM 3.6), frontal lobe adult (RPKM 3.4) and 7 other tissues See more
    Orthologs
    human all
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    Genomic context

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    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

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    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. Sall3 plays essential roles in horizontal cell maturation through regulation of neurofilament expression levels. Baba Y, et al. Biochimie, 2011 Jun. PMID 21396426
    3. 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
    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 (71) 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

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (3)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within forelimb morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within hindlimb morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    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 regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of smoothened signaling pathway 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
    sal-like protein 3
    Names
    sal-like 3
    spalt-like protein 3

    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_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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