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

Gene ID: 6299, updated on 7-Jun-2020

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
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

Genomic context

See SALL1 in Genome Data Viewer
Location:
16q12.1
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (51135975..51151270, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (51169886..51185183, 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 (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study of optic disc parameters.
NHGRI GWA Catalog
Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.
NHGRI GWA Catalog
Weight loss after gastric bypass is associated with a variant at 15q26.1.
NHGRI GWA 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
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
beta-catenin binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adrenal gland development IEP
Inferred from Expression Pattern
more info
PubMed 
branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic digestive tract development IMP
Inferred from Mutant Phenotype
more info
PubMed 
embryonic digit morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
gonad development IEP
Inferred from Expression Pattern
more info
PubMed 
heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
inductive cell-cell signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
kidney epithelium development ISS
Inferred from Sequence or Structural Similarity
more info
 
limb development IMP
Inferred from Mutant Phenotype
more info
PubMed 
mesenchymal to epithelial transition involved in metanephros morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
olfactory bulb interneuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
olfactory bulb mitral cell layer development IMP
Inferred from Mutant Phenotype
more info
PubMed 
olfactory nerve development ISS
Inferred from Sequence or Structural Similarity
more info
 
outer ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
pituitary gland development IEP
Inferred from Expression Pattern
more info
PubMed 
positive regulation of Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
somatic stem cell population maintenance TAS
Traceable Author Statement
more info
 
ureteric bud development ISS
Inferred from Sequence or Structural Similarity
more info
 
ureteric bud invasion ISS
Inferred from Sequence or Structural Similarity
more info
 
ventricular septum development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
chromocenter IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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_001127892.1NP_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
    ENSP00000407914.1, ENST00000440970.5
    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
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    51135975..51151270 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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