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    Sall4 spalt like transcription factor 4 [ Mus musculus (house mouse) ]

    Gene ID: 99377, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Sall4provided by MGI
    Official Full Name
    spalt like transcription factor 4provided by MGI
    Primary source
    MGI:MGI:2139360
    See related
    Ensembl:ENSMUSG00000027547 AllianceGenome:MGI:2139360
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Tex20; 5730441M18Rik; C330011P20Rik
    Summary
    This gene belongs to the spalt family of zinc finger transcription factors. In mouse, functions for this gene have been described in many embryonic developmental processes, including brain, heart, and limb development. In addition, this gene is an important pluripotency factor that is required for stem cell maintenance. Homozygous mutant mice display embryonic lethality, while conditional knock-out in embryonic germ cells results in failure to establish a robust stem cell population. A pseudogene of this gene is found on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
    Expression
    Biased expression in placenta adult (RPKM 3.0), CNS E11.5 (RPKM 2.6) and 8 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Sall4 in Genome Data Viewer
    Location:
    2 H3; 2 88.99 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (168590252..168609121, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (168748332..168767201, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2 Neighboring gene STARR-seq mESC enhancer starr_06462 Neighboring gene STARR-positive B cell enhancer mm9_chr2:168365341-168365641 Neighboring gene STARR-seq mESC enhancer starr_06463 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:168421294-168421477 Neighboring gene STARR-seq mESC enhancer starr_06464 Neighboring gene STARR-seq mESC enhancer starr_06465 Neighboring gene microRNA 7004 Neighboring gene ATPase, class II, type 9A Neighboring gene VISTA enhancer mm1375 Neighboring gene STARR-seq mESC enhancer starr_06468 Neighboring gene STARR-seq mESC enhancer starr_06472 Neighboring gene predicted gene 14261 Neighboring gene predicted gene, 25214 Neighboring gene STARR-positive B cell enhancer ABC_E3422 Neighboring gene zinc finger protein 64 Neighboring gene STARR-positive B cell enhancer ABC_E6025

    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. Stemness factor Sall4 is required for DNA damage response in embryonic stem cells. Xiong J, et al. J Cell Biol, 2015 Mar 2. PMID 25733712, Free PMC Article
    2. Developmental expression of the pluripotency factor sal-like protein 4 in the monkey, human and mouse testis: restriction to premeiotic germ cells. Eildermann K, et al. Cells Tissues Organs, 2012. PMID 22572102
    3. Enhanced self-renewal of hematopoietic stem/progenitor cells mediated by the stem cell gene Sall4. Yang J, et al. J Hematol Oncol, 2011 Sep 23. PMID 21943195, Free PMC Article
    4. SALL4 controls cell fate in response to DNA base composition. Pantier R, et al. Mol Cell, 2021 Feb 18. PMID 33406384, Free PMC Article
    5. Exclusion of Sall 4 as the sex-determining gene in the Mandarin vole Microtus mandarinus mandarinus. Chen Y, et al. Hereditas, 2011 Jun. PMID 21756254

    See all (138) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sall genes regulate hindlimb initiation in mouse embryos.
      Title: Sall genes regulate hindlimb initiation in mouse embryos.
    2. Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm.
      Title: Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm.
    3. SALL4 is a CRL3[REN/KCTD11] substrate that drives Sonic Hedgehog-dependent medulloblastoma.
      Title: SALL4 is a CRL3(REN/KCTD11) substrate that drives Sonic Hedgehog-dependent medulloblastoma.
    4. Sall1 and Sall4 cooperatively interact with Myocd and SRF to promote cardiomyocyte proliferation by regulating CDK and cyclin genes.
      Title: Sall1 and Sall4 cooperatively interact with Myocd and SRF to promote cardiomyocyte proliferation by regulating CDK and cyclin genes.
    5. Sall4 restricts glycolytic metabolism in limb buds through transcriptional regulation of glycolytic enzyme genes.
      Title: Sall4 restricts glycolytic metabolism in limb buds through transcriptional regulation of glycolytic enzyme genes.
    6. Sall4 Guides p53-Mediated Enhancer Interference upon DNA Damage in Mouse Embryonic Stem Cells.
      Title: Sall4 Guides p53-Mediated Enhancer Interference upon DNA Damage in Mouse Embryonic Stem Cells.
    7. Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4.
      Title: Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4.
    8. Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4.
      Title: Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4.
    9. SALL4 controls cell fate in response to DNA base composition.
      Title: SALL4 controls cell fate in response to DNA base composition.
    10. A role of Sall4 in regulating Neuromesodermal progenitor cells and their descendants in mouse embryos.
      Title: Sall4 regulates neuromesodermal progenitors and their descendants during body elongation in mouse embryos.
    Submit: New GeneRIF Correction See all GeneRIFs (50)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within embryonic limb morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within inner cell mass cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neural tube closure IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neural tube development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II 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
    		  
    acts_upstream_of_or_within somatic stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within tissue development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within ventricular septum development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within ventricular septum development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of transcription regulator complex IC
    Inferred by Curator
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sal-like protein 4
    Names
    sal-like 4
    zinc finger protein SALL4

    NCBI Reference Sequences (RefSeq)

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    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_175303.5 → NP_780512.2  sal-like protein 4 isoform a

      See identical proteins and their annotated locations for NP_780512.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) encodes the longest isoform (a).
      Source sequence(s)
      AL929248
      Consensus CDS
      CCDS17115.1
      UniProtKB/Swiss-Prot
      A2AV00, Q6S7E8, Q6S7E9, Q7TST6, Q8BX22
      Related
      ENSMUSP00000029061.6, ENSMUST00000029061.12
      Conserved Domains (4) summary
      cd11674
      Location:796 → 901
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:575 → 595
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:633 → 655
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:587 → 612
      zf-H2C2_2; Zinc-finger double domain

    2. NM_201395.3 → NP_958797.2  sal-like protein 4 isoform b

      See identical proteins and their annotated locations for NP_958797.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) uses an alternate in-frame splice site in an internal exon compared to variant a. It encodes isoform b, which is shorter than isoform a.
      Source sequence(s)
      AK017633, AK049188, BB867997, BC067396, CK341198
      Consensus CDS
      CCDS17116.1
      UniProtKB/Swiss-Prot
      Q8BX22
      UniProtKB/TrEMBL
      Q9CYI8
      Related
      ENSMUSP00000099363.2, ENSMUST00000103074.2
      Conserved Domains (3) summary
      sd00017
      Location:438 → 458
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:436 → 458
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:450 → 475
      zf-H2C2_2; Zinc-finger double domain

    3. NM_201396.3 → NP_958798.2  sal-like protein 4 isoform c

      See identical proteins and their annotated locations for NP_958798.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) lacks an in-frame exon compared to variant (a). It encodes isoform c, which is shorter than isoform a.
      Source sequence(s)
      AK017633, AK049188, BB867997, BC067396, CK341198
      Consensus CDS
      CCDS17117.1
      UniProtKB/Swiss-Prot
      Q8BX22
      UniProtKB/TrEMBL
      Q9CYI8
      Related
      ENSMUSP00000074556.4, ENSMUST00000075044.10
      Conserved Domains (4) summary
      COG5048
      Location:83 → 141
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:93 → 113
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:91 → 113
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:105 → 130
      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_000068.8 Reference GRCm39 C57BL/6J

      Range
      168590252..168609121 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006500486.5 → XP_006500549.1  sal-like protein 4 isoform X1

      Conserved Domains (4) summary
      cd11674
      Location:765 → 870
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:544 → 564
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:602 → 624
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:556 → 581
      zf-H2C2_2; Zinc-finger double domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BX22.2 GenPept UniProtKB/Swiss-Prot:Q8BX22

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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