U.S. flag

An official website of the United States government

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

Gene ID: 6299, updated on 10-Dec-2024

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_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (51135982..51152334, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56933839..56950190, complement)
RS_2024_09 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 superoxide dismutase 1 pseudogene 2 Neighboring gene uncharacterized LOC105371253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:51184378-51184878 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:51188534-51189523 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:51189524-51190512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:51214879-51215686 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:51215687-51216494 Neighboring gene VISTA enhancer hs76 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:51324751-51325261 Neighboring gene uracil-DNA glycosylase pseudogene 1 Neighboring gene uncharacterized LOC107984886

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

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

General gene information

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in adrenal gland development PubMed 
involved_in branching involved in ureteric bud morphogenesis  
involved_in embryonic digestive tract development PubMed 
involved_in embryonic digit morphogenesis PubMed 
involved_in gonad development PubMed 
involved_in heart development PubMed 
involved_in inductive cell-cell signaling  
involved_in kidney development PubMed 
involved_in kidney epithelium development  
involved_in limb development PubMed 
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis PubMed 
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in olfactory bulb interneuron differentiation  
involved_in olfactory bulb mitral cell layer development PubMed 
involved_in olfactory nerve development  
involved_in pituitary gland development PubMed 
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of Wnt signaling pathway PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in regulation of transcription by RNA polymerase II  
involved_in ureteric bud development  
involved_in ureteric bud invasion  
involved_in ventricular septum development  
Component Evidence Code Pubs
located_in chromocenter PubMed 
located_in cytoplasm PubMed 
located_in heterochromatin PubMed 
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus 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/TrEMBL
    H3BSM9
    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
    Q99881, Q9NSC2, Q9NSC3, Q9P1R0
    UniProtKB/TrEMBL
    V9HVY5
    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_2024_08

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
    Q99881, Q9NSC2, Q9NSC3, Q9P1R0
    UniProtKB/TrEMBL
    V9HVY5
    Related
    ENSP00000407914.2, ENST00000440970.6
  2. XM_047434442.1XP_047290398.1  sal-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q99881, Q9NSC2, Q9NSC3, Q9P1R0
    UniProtKB/TrEMBL
    V9HVY5
    Related
    ENSP00000509873.1, ENST00000685868.1
  3. XM_047434444.1XP_047290400.1  sal-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q99881, Q9NSC2, Q9NSC3, Q9P1R0
    UniProtKB/TrEMBL
    V9HVY5

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

    UniProtKB/TrEMBL
    V9HVY5
  2. XM_054313589.1XP_054169564.1  sal-like protein 1 isoform X1

    UniProtKB/TrEMBL
    V9HVY5
External link. Please review our privacy policy.