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

    Gene ID: 99377, updated on 2-Oct-2018

    Summary

    Official Symbol
    Sall4provided by MGI
    Official Full Name
    spalt like transcription factor 4provided by MGI
    Primary source
    MGI:MGI:2139360
    See related
    Ensembl:ENSMUSG00000027547 Vega:OTTMUSG00000016116
    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; C78083; C78563; AA407717; AL022809; AW536104; 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

    Genomic context

    See Sall4 in Genome Data Viewer
    Location:
    2 H3; 2 88.99 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (168748332..168767201, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (168573832..168592701, complement)

    Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2 Neighboring gene microRNA 7004 Neighboring gene ATPase, class II, type 9A Neighboring gene predicted gene 14261 Neighboring gene predicted gene, 38422 Neighboring gene zinc finger protein 64

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

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

    Pathways from BioSystems

    • PluriNetWork, organism-specific biosystem (from WikiPathways)
      PluriNetWork, organism-specific biosystemThe aim of the PluriNetWork is to give an overview of specific mechanisms associated with pluripotency in mouse. Each node represents a gene and its corresponding protein product. As stated, we inten...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

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

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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_175303.4NP_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) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK017633, AK049188, BB867997, BC067396, CK341198
      Consensus CDS
      CCDS17115.1
      UniProtKB/Swiss-Prot
      Q8BX22
      UniProtKB/TrEMBL
      Q9CYI8
      Related
      ENSMUSP00000029061.5, OTTMUSP00000017238, ENSMUST00000029061.11, OTTMUST00000038511
      Conserved Domains (4) summary
      cd11674
      Location:796901
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:575595
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:633655
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:587612
      zf-H2C2_2; Zinc-finger double domain
    2. NM_201395.3NP_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
      ENSMUSP00000099363.1, OTTMUSP00000017239, ENSMUST00000103074.1, OTTMUST00000038512
      Conserved Domains (3) summary
      sd00017
      Location:438458
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:436458
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:450475
      zf-H2C2_2; Zinc-finger double domain
    3. NM_201396.3NP_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
      ENSMUSP00000074556.3, OTTMUSP00000017241, ENSMUST00000075044.9, OTTMUST00000038515
      Conserved Domains (4) summary
      COG5048
      Location:83141
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:93113
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:91113
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:105130
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      168748332..168767201 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006500486.3XP_006500549.1  sal-like protein 4 isoform X1

      Conserved Domains (4) summary
      cd11674
      Location:765870
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:544564
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:602624
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:556581
      zf-H2C2_2; Zinc-finger double domain
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