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

Gene ID: 99377, updated on 8-Jul-2018
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
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

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region DNA binding IBA
Inferred from Biological aspect of Ancestor
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 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
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 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
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 
Preferred Names
sal-like protein 4
Names
sal-like 4
zinc finger protein SALL4

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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