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    SALL1 spalt like transcription factor 1 [ Homo sapiens (human) ]

    Gene ID: 6299, updated on 21-Mar-2023

    Summary

    Official Symbol
    SALL1provided by HGNC
    Official Full Name
    spalt like transcription factor 1provided by HGNC
    Primary source
    HGNC:HGNC:10524
    See related
    Ensembl:ENSG00000103449 MIM:602218; AllianceGenome:HGNC:10524
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TBS; HSAL1; Sal-1; ZNF794; HEL-S-89
    Summary
    The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 14.2), thyroid (RPKM 12.6) and 8 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SALL1 in Genome Data Viewer
    Location:
    16q12.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (51135982..51152334, complement)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56933839..56950190, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (51169893..51185181, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs152 Neighboring gene uncharacterized LOC105371253 Neighboring gene VISTA enhancer hs76 Neighboring gene uracil-DNA glycosylase pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Townes-Brocks syndrome 1
    MedGen: C4551481 OMIM: 107480 GeneReviews: Townes-Brocks Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-01-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2021-01-27)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study of optic disc parameters.
    EBI GWAS Catalog
    Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.
    EBI GWAS Catalog
    Weight loss after gastric bypass is associated with a variant at 15q26.1.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables beta-catenin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adrenal gland development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in embryonic digestive tract development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic digit morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gonad development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in inductive cell-cell signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in kidney development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in kidney epithelium development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in limb development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription 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 
    involved_in olfactory bulb interneuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in olfactory bulb mitral cell layer development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in olfactory nerve development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pituitary gland development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in ureteric bud development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ureteric bud invasion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ventricular septum development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in chromocenter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    sal-like protein 1
    Names
    epididymis secretory protein Li 89
    zinc finger protein 794
    zinc finger protein SALL1
    zinc finger protein Spalt-1

    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.

    Genomic

    1. NG_007990.1 RefSeqGene

      Range
      5001..20298
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_674

    mRNA and Protein(s)

    1. NM_001127892.2NP_001121364.1  sal-like protein 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC009166, AK307835, Y18265
      Consensus CDS
      CCDS45483.1
      UniProtKB/Swiss-Prot
      Q9NSC2
      Related
      ENSP00000456777.2, ENST00000570206.2
      Conserved Domains (5) summary
      cd11674
      Location:9671058
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:611631
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:906926
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:10371059
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:623648
      zf-H2C2_2; Zinc-finger double domain
    2. NM_002968.3NP_002959.2  sal-like protein 1 isoform a

      See identical proteins and their annotated locations for NP_002959.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC009166, BP229682, DA318592
      Consensus CDS
      CCDS10747.1
      UniProtKB/Swiss-Prot
      Q9NSC2, Q9P1R0
      Related
      ENSP00000251020.4, ENST00000251020.9
      Conserved Domains (5) summary
      cd11674
      Location:10641155
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:708728
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:10031023
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:11341156
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:720745
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      51135982..51152334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434443.1XP_047290399.1  sal-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9P1R0
      Related
      ENSP00000407914.2, ENST00000440970.6
    2. XM_047434442.1XP_047290398.1  sal-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9P1R0
      Related
      ENSP00000509873.1, ENST00000685868.1
    3. XM_047434444.1XP_047290400.1  sal-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9P1R0

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      56933839..56950190 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313590.1XP_054169565.1  sal-like protein 1 isoform X1

    2. XM_054313589.1XP_054169564.1  sal-like protein 1 isoform X1