Human Gene SALL1 (ENST00000251020.9) from GENCODE V44
  Description: Homo sapiens spalt like transcription factor 1 (SALL1), transcript variant 1, mRNA. (from RefSeq NM_002968)
RefSeq Summary (NM_002968): 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].
Gencode Transcript: ENST00000251020.9
Gencode Gene: ENSG00000103449.13
Transcript (Including UTRs)
   Position: hg38 chr16:51,135,982-51,151,270 Size: 15,289 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg38 chr16:51,137,112-51,151,241 Size: 14,130 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:51,135,982-51,151,270)mRNA (may differ from genome)Protein (1324 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Sal-like protein 1; AltName: Full=Spalt-like transcription factor 1; AltName: Full=Zinc finger protein 794; AltName: Full=Zinc finger protein SALL1; AltName: Full=Zinc finger protein Spalt-1; Short=HSal1; Short=Sal-1;
FUNCTION: Transcriptional repressor involved in organogenesis (By similarity).
SUBUNIT: Interacts with HDAC1, HDAC2, RBBP4, RBPP7, MTA1 and MTA2 (By similarity). Interacts with FAM58A. Probably associates with NuRD histone deacetylase complex (HDAC).
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Highest levels in kidney. Lower levels in adult brain (enriched in corpus callosum, lower expression in substantia nigra) and liver.
DEVELOPMENTAL STAGE: In fetal brain exclusively in neurons of the subependymal region of hypothalamus lateral to the third ventricle.
DISEASE: Defects in SALL1 are the cause of Townes-Brocks syndrome (TBS) [MIM:107480]. TBS is a rare, autosomal dominant malformation syndrome with a combination of imperforate anus, triphalangeal and supernumerary thumbs, malformed ears and sensorineural hearing loss. Note=Some individuals with SALL1 mutations manifest a phenotype overlapping with TBS and bronchio-oto-renal syndrome. Clinical features include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux, hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or hand malformations of TBS.
SIMILARITY: Belongs to the sal C2H2-type zinc-finger protein family.
SIMILARITY: Contains 9 C2H2-type zinc fingers.
WEB RESOURCE: Name=GeneReviews; URL="";

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: SALL1
Diseases sorted by gene-association score: townes-brocks syndrome 1* (919), townes-brocks syndrome* (914), duane-radial ray syndrome (26), imperforate anus (18), mosaic trisomy 8 (18), hemifacial microsomia (17), inverted follicular keratosis (16), tuberculous empyema (11), renal hypodysplasia/aplasia 1 (10), melanoacanthoma (9), autosomal dominant disease (9), lung sarcoma (9), renal dysplasia (7), renal hypodysplasia (7), vestibulocochlear nerve disease (7), vestibular neuronitis (7), branchiootorenal syndrome (6), baller-gerold syndrome (5), keratosis, seborrheic, somatic (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.28 RPKM in Thyroid
Total median expression: 181.23 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.8029-0.097 Picture PostScript Text
3' UTR -256.101130-0.227 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

ModBase Predicted Comparative 3D Structure on Q9NSC2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0046872 metal ion binding
GO:0004407 histone deacetylase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001657 ureteric bud development
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0001822 kidney development
GO:0003281 ventricular septum development
GO:0003337 mesenchymal to epithelial transition involved in metanephros morphogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007507 heart development
GO:0008406 gonad development
GO:0016575 histone deacetylation
GO:0021553 olfactory nerve development
GO:0021889 olfactory bulb interneuron differentiation
GO:0021983 pituitary gland development
GO:0022008 neurogenesis
GO:0030177 positive regulation of Wnt signaling pathway
GO:0030325 adrenal gland development
GO:0031129 inductive cell-cell signaling
GO:0035019 somatic stem cell population maintenance
GO:0042473 outer ear morphogenesis
GO:0042733 embryonic digit morphogenesis
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048566 embryonic digestive tract development
GO:0060173 limb development
GO:0061034 olfactory bulb mitral cell layer development
GO:0072073 kidney epithelium development
GO:0072092 ureteric bud invasion

Cellular Component:
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0010369 chromocenter
GO:0016581 NuRD complex

-  Descriptions from all associated GenBank mRNAs
  EU668343 - Homo sapiens epididymis secretory protein Li 89 (HEL-S-89) mRNA, complete cds.
Y18265 - Homo sapiens mRNA for zinc finger protein SALL1.
JD552907 - Sequence 533931 from Patent EP1572962.
AK295103 - Homo sapiens cDNA FLJ55320 complete cds, highly similar to Sal-like protein 1.
JD362850 - Sequence 343874 from Patent EP1572962.
JD315160 - Sequence 296184 from Patent EP1572962.
JD058736 - Sequence 39760 from Patent EP1572962.
BC113881 - Homo sapiens sal-like 1 (Drosophila), mRNA (cDNA clone IMAGE:40081793), complete cds.
BC113906 - Homo sapiens sal-like 1 (Drosophila), mRNA (cDNA clone IMAGE:40081792), complete cds.
BC131548 - Homo sapiens sal-like 1 (Drosophila), mRNA (cDNA clone IMAGE:40081794), complete cds.
JD408645 - Sequence 389669 from Patent EP1572962.
BC167772 - Synthetic construct Homo sapiens clone IMAGE:100068162, MGC:195779 sal-like 1 (Drosophila) (SALL1) mRNA, encodes complete protein.
AK307835 - Homo sapiens cDNA, FLJ97783.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NSC2 (Reactome details) participates in the following event(s):

R-HSA-2892247 POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
R-HSA-452723 Transcriptional regulation of pluripotent stem cells
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000251020.1, ENST00000251020.2, ENST00000251020.3, ENST00000251020.4, ENST00000251020.5, ENST00000251020.6, ENST00000251020.7, ENST00000251020.8, NM_002968, Q99881, Q9NSC2, Q9NSC3, Q9P1R0, SAL1, SALL1_HUMAN, uc059ucs.1, uc059ucs.2, ZNF794
UCSC ID: ENST00000251020.9
RefSeq Accession: NM_002968
Protein: Q9NSC2 (aka SALL1_HUMAN or SAL1_HUMAN)
CCDS: CCDS10747.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SALL1:
tbs (Townes-Brocks Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.