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Sall1 spalt like transcription factor 1 [ Mus musculus (house mouse) ]

Gene ID: 58198, updated on 24-Jan-2023

Summary

Official Symbol
Sall1provided by MGI
Official Full Name
spalt like transcription factor 1provided by MGI
Primary source
MGI:MGI:1889585
See related
Ensembl:ENSMUSG00000031665 AllianceGenome:MGI:1889585
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
Msal-3
Summary
Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of ectoderm development; negative regulation of mesoderm development; and nephron epithelium morphogenesis. Acts upstream of or within several processes, including limb morphogenesis; nervous system development; and regulation of transcription by RNA polymerase II. Located in heterochromatin and nucleus. Part of NuRD complex. Is expressed in several structures, including autopod; central nervous system; embryo mesenchyme; metanephros; and sensory organ. Used to study Townes-Brocks syndrome. Human ortholog(s) of this gene implicated in Townes-Brocks syndrome and middle lobe syndrome. Orthologous to human SALL1 (spalt like transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in frontal lobe adult (RPKM 12.3), kidney adult (RPKM 12.2) and 16 other tissues See more
Orthologs
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Genomic context

See Sall1 in Genome Data Viewer
Location:
8; 8 C3
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (89753867..89770790, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (89027242..89044162, complement)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated Sall1 enhancer cluster Neighboring gene microRNA 8110 Neighboring gene predicted gene 3134 Neighboring gene predicted gene, 35358 Neighboring gene predicted gene, 35305

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

Homology

Gene Ontology Provided by MGI

Process Evidence Code Pubs
acts_upstream_of GABAergic neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of branching involved in ureteric bud morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in branching involved in ureteric bud morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic digestive tract development ISO
Inferred from Sequence Orthology
more info
 
involved_in embryonic digit morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic digit morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within forelimb morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in heart development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within hindlimb morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within inductive cell-cell signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney development ISO
Inferred from Sequence Orthology
more info
 
involved_in kidney epithelium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in limb development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of mesenchymal to epithelial transition involved in metanephros morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of ectoderm development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of mesoderm development IMP
Inferred from Mutant Phenotype
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 negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within neural tube closure IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within neural tube development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within olfactory bulb development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in olfactory bulb interneuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in olfactory bulb mitral cell layer development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within olfactory nerve development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of branching involved in ureteric bud morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of neuroblast proliferation 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
PubMed 
acts_upstream_of smoothened signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ureteric bud development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ureteric bud invasion IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ureteric bud invasion IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ventricular septum development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in ventricular septum development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of NuRD complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromocenter ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in heterochromatin ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IC
Inferred by Curator
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
sal-like protein 1
Names
sal-3
sal-like 1
zinc finger protein Spalt-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_001371069.1NP_001357998.1  sal-like protein 1

    Status: VALIDATED

    Source sequence(s)
    AC147558
    Consensus CDS
    CCDS40427.1
    UniProtKB/TrEMBL
    Q6P5E3
    Conserved Domains (6) summary
    COG5048
    Location:7001168
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:707727
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:10021022
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:10281050
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:719744
    zf-H2C2_2; Zinc-finger double domain
    cd20908
    Location:449536
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  2. NM_001371070.1NP_001357999.1  sal-like protein 1

    Status: VALIDATED

    Source sequence(s)
    AC147558
    Consensus CDS
    CCDS40427.1
    UniProtKB/TrEMBL
    Q6P5E3
    Conserved Domains (6) summary
    COG5048
    Location:7001168
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:707727
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:10021022
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:10281050
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:719744
    zf-H2C2_2; Zinc-finger double domain
    cd20908
    Location:449536
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  3. NM_021390.3NP_067365.2  sal-like protein 1

    See identical proteins and their annotated locations for NP_067365.2

    Status: VALIDATED

    Source sequence(s)
    BC062937
    Consensus CDS
    CCDS40427.1
    UniProtKB/TrEMBL
    Q6P5E3
    Related
    ENSMUSP00000034090.7, ENSMUST00000034090.8
    Conserved Domains (6) summary
    COG5048
    Location:7001168
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:707727
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:10021022
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:10281050
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:719744
    zf-H2C2_2; Zinc-finger double domain
    cd20908
    Location:449536
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    89753867..89770790 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036154203.1XP_036010096.1  sal-like protein 1 isoform X1

    Conserved Domains (6) summary
    COG5048
    Location:6031071
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:610630
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:905925
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:931953
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:622647
    zf-H2C2_2; Zinc-finger double domain
    cd20908
    Location:352439
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins