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Aliases for SALL3 Gene

Aliases for SALL3 Gene

  • Spalt Like Transcription Factor 3 2 3 5
  • Zinc Finger Protein 796 3 4
  • ZNF796 3 4
  • HSALL3 3 4
  • C2H2 Zinc Finger Protein SALL3 3
  • Spalt-Like Zinc Finger Protein 3
  • Zinc Finger Protein SALL3 4
  • Sal (Drosophila)-Like 3 2
  • Sal-Like 3 (Drosophila) 2
  • Sal-Like Protein 3 3

External Ids for SALL3 Gene

Previous GeneCards Identifiers for SALL3 Gene

  • GC18U990052
  • GC18P076766
  • GC18P076475
  • GC18P074839
  • GC18P074841
  • GC18P073383

Summaries for SALL3 Gene

Entrez Gene Summary for SALL3 Gene

  • This gene encodes a sal-like C2H2-type zinc-finger protein, and belongs to a family of evolutionarily conserved genes found in species as diverse as Drosophila, C. elegans, and vertebrates. Mutations in some of these genes are associated with congenital disorders in human, suggesting their importance in embryonic development. This protein binds to DNA methyltransferase 3 alpha (DNMT3A), and reduces DNMT3A-mediated CpG island methylation. It is suggested that silencing of this gene, resulting in acceleration of DNA methylation, may have a role in oncogenesis. [provided by RefSeq, Oct 2011]

GeneCards Summary for SALL3 Gene

SALL3 (Spalt Like Transcription Factor 3) is a Protein Coding gene. An important paralog of this gene is SALL1.

UniProtKB/Swiss-Prot for SALL3 Gene

  • Probable transcription factor.

Gene Wiki entry for SALL3 Gene

Additional gene information for SALL3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SALL3 Gene

Genomics for SALL3 Gene

GeneHancer (GH) Regulatory Elements for SALL3 Gene

Promoters and enhancers for SALL3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18I078980 Promoter/Enhancer 1.4 UCNEbase EPDnew ENCODE 550.8 +1.1 1083 2.3 ZNF335 POLR2A POU5F1 EZH2 ZBTB20 LINC01896 SALL3 ATP9B
GH18I078978 Enhancer 0.4 ENCODE 550.8 -1.5 -1534 0.1 POLR2A EZH2 LINC01896 SALL3 ENSG00000265101
GH18I078981 Enhancer 0.4 ENCODE 550.8 -1.0 -969 0.3 ZNF398 EZH2 LINC01896 SALL3 ENSG00000265101
GH18I078979 Enhancer 0.2 ENCODE 550.8 -0.2 -219 0.2 LINC01896 SALL3
GH18I078814 Enhancer 0.2 FANTOM5 4.7 -165.4 -165400 0.2 SALL3 ENSG00000266273 GC18M078901 PIR40267
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SALL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SALL3 gene promoter:

Genomic Locations for SALL3 Gene

Genomic Locations for SALL3 Gene
22,403 bases
Plus strand

Genomic View for SALL3 Gene

Genes around SALL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SALL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SALL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SALL3 Gene

Proteins for SALL3 Gene

  • Protein details for SALL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sal-like protein 3
    Protein Accession:
    Secondary Accessions:
    • Q9UGH1

    Protein attributes for SALL3 Gene

    1300 amino acids
    Molecular mass:
    135346 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SALL3 Gene


neXtProt entry for SALL3 Gene

Post-translational modifications for SALL3 Gene

  • Ubiquitination at posLast=11981198

Other Protein References for SALL3 Gene

No data available for DME Specific Peptides for SALL3 Gene

Domains & Families for SALL3 Gene

Gene Families for SALL3 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SALL3 Gene

Suggested Antigen Peptide Sequences for SALL3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the sal C2H2-type zinc-finger protein family.
  • Belongs to the sal C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with SALL3: view

Function for SALL3 Gene

Molecular function for SALL3 Gene

GENATLAS Biochemistry:
spalt (sal)-like,Drosophila SAL like gene 3,expressed in fetal brain and in several adult tissues,haploinsufficency in the 18q deletion syndrome and may be contributing to the phenotype
UniProtKB/Swiss-Prot Function:
Probable transcription factor.

Phenotypes From GWAS Catalog for SALL3 Gene

Gene Ontology (GO) - Molecular Function for SALL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IBA --
GO:0043565 sequence-specific DNA binding IBA --
GO:0044212 transcription regulatory region DNA binding IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SALL3: view
genes like me logo Genes that share phenotypes with SALL3: view

Animal Models for SALL3 Gene

MGI Knock Outs for SALL3:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SALL3 Gene

Localization for SALL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SALL3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SALL3 gene
Compartment Confidence
nucleus 3

Gene Ontology (GO) - Cellular Components for SALL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with SALL3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SALL3 Gene

Pathways & Interactions for SALL3 Gene

SuperPathways for SALL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SALL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA --
GO:0006366 transcription by RNA polymerase II IBA --
GO:0007165 signal transduction IBA --
GO:0021891 olfactory bulb interneuron development IEA --
genes like me logo Genes that share ontologies with SALL3: view

No data available for Pathways by source and SIGNOR curated interactions for SALL3 Gene

Drugs & Compounds for SALL3 Gene

No Compound Related Data Available

Transcripts for SALL3 Gene

mRNA/cDNA for SALL3 Gene

Unigene Clusters for SALL3 Gene

Sal-like 3 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SALL3 Gene

No ASD Table

Relevant External Links for SALL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SALL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SALL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SALL3 Gene

This gene is overexpressed in Vagina (x6.1), Brain - Spinal cord (cervical c-1) (x5.5), Brain - Caudate (basal ganglia) (x4.4), Brain - Amygdala (x4.2), and Brain - Nucleus accumbens (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for SALL3 Gene

This gene is overexpressed in Saliva (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SALL3 Gene

Protein tissue co-expression partners for SALL3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SALL3 Gene:


SOURCE GeneReport for Unigene cluster for SALL3 Gene:


mRNA Expression by UniProt/SwissProt for SALL3 Gene:

Tissue specificity: Widely expressed in adult with highest levels in heart. Expressed in fetal brain (in neurons of hippocampus, cortex, mediodorsal and ventrolateral thalamic nuclei, putamen, cerebellum and brainstem).
genes like me logo Genes that share expression patterns with SALL3: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SALL3 Gene

Orthologs for SALL3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SALL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SALL3 33 34
  • 98.4 (n)
(Ornithorhynchus anatinus)
Mammalia SALL3 34
  • 85 (a)
(Bos Taurus)
Mammalia SALL3 33
  • 83.16 (n)
(Canis familiaris)
Mammalia SALL3 34
  • 81 (a)
(Rattus norvegicus)
Mammalia Sall3 33
  • 80.99 (n)
(Mus musculus)
Mammalia Sall3 33 16 34
  • 79 (n)
(Monodelphis domestica)
Mammalia SALL3 34
  • 77 (a)
(Gallus gallus)
Aves SALL3 33 34
  • 71.51 (n)
(Anolis carolinensis)
Reptilia SALL3 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sall3 33
  • 65.82 (n)
African clawed frog
(Xenopus laevis)
Amphibia sal1-A 33
(Danio rerio)
Actinopterygii LOC560775 33
  • 65.3 (n)
sall3a 34
  • 56 (a)
sall3b 34
  • 53 (a)
fruit fly
(Drosophila melanogaster)
Insecta salr 34
  • 27 (a)
salm 34
  • 26 (a)
(Caenorhabditis elegans)
Secernentea sem-4 34
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FZF1 34
  • 27 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
-- 34
  • 25 (a)
Species where no ortholog for SALL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SALL3 Gene

Gene Tree for SALL3 (if available)
Gene Tree for SALL3 (if available)

Paralogs for SALL3 Gene

Paralogs for SALL3 Gene Pseudogenes for SALL3 Gene

genes like me logo Genes that share paralogs with SALL3: view

Variants for SALL3 Gene

Sequence variations from dbSNP and Humsavar for SALL3 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs760494400 likely-benign, Anophthalmia - microphthalmia 78,994,245(+) G/A/C coding_sequence_variant, missense_variant
VAR_035552 A colorectal cancer sample p.Arg143His
rs1000181112 -- 78,997,651(+) T/C 3_prime_UTR_variant
rs1000347523 -- 78,987,444(+) C/A intron_variant
rs1000553009 -- 78,999,225(+) G/A/C downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SALL3 Gene

Variant ID Type Subtype PubMed ID
nsv577793 CNV loss 21841781
nsv577794 CNV gain 21841781
nsv577795 CNV loss 21841781
nsv577796 CNV loss 21841781
nsv577799 CNV gain+loss 21841781
nsv577800 CNV loss 21841781
nsv577821 CNV loss 21841781
nsv828333 CNV loss 20364138
nsv828338 CNV gain 20364138
nsv458313 CNV loss 19166990
nsv2377 CNV insertion 18451855
nsv1143887 CNV deletion 24896259
nsv1141945 CNV deletion 24896259
nsv1133432 CNV deletion 24896259
nsv1071874 CNV deletion 25765185
nsv1065902 CNV gain 25217958
esv3643278 CNV gain 21293372
esv3643277 CNV loss 21293372
esv29012 CNV loss 19812545
esv2717497 CNV deletion 23290073
esv2666555 CNV deletion 23128226
dgv6104n54 CNV gain+loss 21841781
dgv6103n54 CNV loss 21841781
dgv6102n54 CNV gain+loss 21841781
dgv6101n54 CNV gain 21841781
dgv6100n54 CNV loss 21841781
dgv6099n54 CNV gain 21841781
dgv565n67 CNV gain 20364138
dgv564n67 CNV gain 20364138
nsv828342 CNV gain 20364138

Variation tolerance for SALL3 Gene

Residual Variation Intolerance Score: 37.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.15; 69.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SALL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SALL3 Gene

Disorders for SALL3 Gene

Additional Disease Information for SALL3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SALL3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SALL3 Gene

Publications for SALL3 Gene

  1. SALL3, a new member of the human spalt-like gene family, maps to 18q23. (PMID: 10610715) Kohlhase J … Engel W (Genomics 1999) 2 3 4 58
  2. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 44 58
  3. Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. (PMID: 18668548) Julià A … Marsal S (Arthritis and rheumatism 2008) 3 44 58
  4. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. (PMID: 26687479) Oliviero G … Cagney G (Scientific reports 2015) 3 58
  5. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. (PMID: 23535732) Eeles RA … Easton DF (Nature genetics 2013) 3 58

Products for SALL3 Gene

Sources for SALL3 Gene

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