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

Gene ID: 99377, updated on 10-Jun-2024

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 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
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Genomic context

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

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 Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
part_of 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 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

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

NCBI Reference Sequences (RefSeq)

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_175303.5NP_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: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
    ENSMUSP00000099363.2, ENSMUST00000103074.2
    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
    ENSMUSP00000074556.4, ENSMUST00000075044.10
    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: 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_006500486.5XP_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