This gene encodes a zinc finger transcription factor thought to play a role in the development of abducens motor neurons. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015] See more...

Aliases for SALL4 Gene

Aliases for SALL4 Gene

  • Spalt Like Transcription Factor 4 2 3 5
  • Zinc Finger Protein SALL4 3 4
  • Zinc Finger Protein 797 3 4
  • Sal-Like Protein 4 3 4
  • ZNF797 3 4
  • Sal (Drosophila)-Like 4 2
  • Sal-Like 4 (Drosophila) 2
  • HSAL4 3
  • DRRS 3

External Ids for SALL4 Gene

Previous GeneCards Identifiers for SALL4 Gene

  • GC20M050129
  • GC20M051039
  • GC20M051086
  • GC20M049833
  • GC20M050400
  • GC20M047147

Summaries for SALL4 Gene

Entrez Gene Summary for SALL4 Gene

  • This gene encodes a zinc finger transcription factor thought to play a role in the development of abducens motor neurons. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

GeneCards Summary for SALL4 Gene

SALL4 (Spalt Like Transcription Factor 4) is a Protein Coding gene. Diseases associated with SALL4 include Duane-Radial Ray Syndrome and Ivic Syndrome. Among its related pathways are Transcriptional regulation of pluripotent stem cells and Regulation of Wnt-mediated beta catenin signaling and target gene transcription. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is SALL3.

UniProtKB/Swiss-Prot Summary for SALL4 Gene

  • Transcription factor with a key role in the maintenance and self-renewal of embryonic and hematopoietic stem cells.

Gene Wiki entry for SALL4 Gene

Additional gene information for SALL4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SALL4 Gene

Genomics for SALL4 Gene

GeneHancer (GH) Regulatory Elements for SALL4 Gene

Promoters and enhancers for SALL4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J051797 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 527 +113.1 113075 6.2 ZNF217 CTCF TEAD4 ZIC2 SAP30 RFX1 CUX1 CHD1 TGIF2 EP300 SALL4 lnc-ATP9A-1 ADNP RNU7-6P ATP9A ZFP64 piR-43105-389
GH20J051862 Promoter/Enhancer 0.7 EPDnew Ensembl 500.2 +50.3 50344 1 ESRRA MYC SREBF1 LINC01429 piR-59425-021 SALL4 ATP9A RF00017-3634
GH20J051914 Enhancer 0.5 Ensembl 500.7 -1.6 -1556 0.4 MXI1 ZBTB17 RCOR1 RFX5 CHD2 GATA2 POLR2A SALL4 lnc-ZFP64-9
GH20J051810 Enhancer 1.1 Ensembl ENCODE 11.9 +101.5 101544 3 EP300 CTCF NCOR1 FOS KDM6A TCF7 ZBTB25 CHD1 SMARCC2 SKI SALL4 piR-50437-414 lnc-ATP9A-1
GH20J051741 Enhancer 1.3 Ensembl ENCODE dbSUPER 5.1 +169.3 169344 5.8 EP300 ZNF217 ZSCAN5C TCF12 NCOR1 ZIC2 KDM6A CLOCK TCF7 FOXA1 ATP9A SALL4 LOC100419570 lnc-MOCS3-6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SALL4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SALL4

Top Transcription factor binding sites by QIAGEN in the SALL4 gene promoter:
  • AhR
  • Arnt
  • Cdc5
  • CUTL1
  • NF-1
  • Pax-5
  • Pbx1a
  • POU6F1 (c2)

Genomic Locations for SALL4 Gene

Genomic Locations for SALL4 Gene
chr20:51,782,331-51,913,245
(GRCh38/hg38)
Size:
130,915 bases
Orientation:
Minus strand
chr20:50,400,581-50,419,059
(GRCh37/hg19)
Size:
18,479 bases
Orientation:
Minus strand

Genomic View for SALL4 Gene

Genes around SALL4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SALL4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SALL4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SALL4 Gene

Proteins for SALL4 Gene

  • Protein details for SALL4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UJQ4-SALL4_HUMAN
    Recommended name:
    Sal-like protein 4
    Protein Accession:
    Q9UJQ4
    Secondary Accessions:
    • A2A2D8
    • Q540H3
    • Q6Y8G6

    Protein attributes for SALL4 Gene

    Size:
    1053 amino acids
    Molecular mass:
    112231 Da
    Quaternary structure:
    • Interacts with NANOG (By similarity). Interacts with POU5F1/OCT4. Interacts with BEND3.

    Three dimensional structures from OCA and Proteopedia for SALL4 Gene

    Alternative splice isoforms for SALL4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SALL4 Gene

Post-translational modifications for SALL4 Gene

  • Isoform SALL4B exists primarily as a ubiquitinated form.
  • Sumoylation with both SUMO1 and SUMO2 regulates the stability, subcellular localization, transcriptional activity, and may reduce interaction with POU5F1/OCT4.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SALL4 Gene

No data available for DME Specific Peptides for SALL4 Gene

Domains & Families for SALL4 Gene

Gene Families for SALL4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SALL4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SALL4 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger protein SALL4 (SALL4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UJQ4

UniProtKB/Swiss-Prot:

SALL4_HUMAN :
  • Belongs to the sal C2H2-type zinc-finger protein family.
Family:
  • Belongs to the sal C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with SALL4: view

Function for SALL4 Gene

Molecular function for SALL4 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor with a key role in the maintenance and self-renewal of embryonic and hematopoietic stem cells.

Phenotypes From GWAS Catalog for SALL4 Gene

Gene Ontology (GO) - Molecular Function for SALL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 21914818
GO:0008134 transcription factor binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SALL4: view
genes like me logo Genes that share phenotypes with SALL4: view

Human Phenotype Ontology for SALL4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SALL4 Gene

MGI Knock Outs for SALL4:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SALL4 Gene

Localization for SALL4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SALL4 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
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 SALL4 gene
Compartment Confidence
nucleus 5
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SALL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000792 heterochromatin IEA --
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA --
GO:0032991 protein-containing complex IEA --
genes like me logo Genes that share ontologies with SALL4: view

Pathways & Interactions for SALL4 Gene

genes like me logo Genes that share pathways with SALL4: view

SIGNOR curated interactions for SALL4 Gene

Activates:
Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for SALL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001701 in utero embryonic development IEA --
GO:0001833 inner cell mass cell proliferation IEA --
GO:0001843 neural tube closure IEA --
GO:0003281 ventricular septum development IEA --
genes like me logo Genes that share ontologies with SALL4: view

Drugs & Compounds for SALL4 Gene

(1) Drugs for SALL4 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SALL4: view

Transcripts for SALL4 Gene

mRNA/cDNA for SALL4 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SALL4 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d · 5e ^ 6 ^ 7a · 7b
SP1: - - - - - -
SP2: - -
SP3: - - - - - - -
SP4: - - - - - - - - - - -
SP5: - -
SP6:

Relevant External Links for SALL4 Gene

GeneLoc Exon Structure for
SALL4

Expression for SALL4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SALL4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SALL4 Gene

This gene is overexpressed in Thyroid (x12.2), Testis (x8.2), Pancreas (x4.7), and Prostate (x4.3).

Protein differential expression in normal tissues from HIPED for SALL4 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SALL4 Gene



Protein tissue co-expression partners for SALL4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SALL4

SOURCE GeneReport for Unigene cluster for SALL4 Gene:

Hs.517113

mRNA Expression by UniProt/SwissProt for SALL4 Gene:

Q9UJQ4-SALL4_HUMAN
Tissue specificity: Expressed in testis. Constitutively expressed in acute myeloid leukemia (AML).

Phenotype-based relationships between genes and organs from Gene ORGANizer for SALL4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • mouth
  • nose
  • outer ear
  • pharynx
  • skull
Thorax:
  • chest wall
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
Abdomen:
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • anus
  • pelvis
  • rectum
  • ureter
  • urinary bladder
  • vagina
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shoulder
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with SALL4: view

No data available for Evidence on tissue expression from TISSUES for SALL4 Gene

Orthologs for SALL4 Gene

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

Orthologs for SALL4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SALL4 31 30
  • 99.62 (n)
OneToOne
dog
(Canis familiaris)
Mammalia -- 31
  • 87 (a)
OneToMany
SALL4 30
  • 86.24 (n)
cow
(Bos Taurus)
Mammalia SALL4 31 30
  • 80.73 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sall4 30
  • 78.83 (n)
mouse
(Mus musculus)
Mammalia Sall4 17 31 30
  • 78.54 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SALL4 31
  • 62 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SALL4 31
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves SALL4 31 30
  • 66.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SALL4 31
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sall4 30
  • 58.73 (n)
Str.6496 30
African clawed frog
(Xenopus laevis)
Amphibia SALL4 30
zebrafish
(Danio rerio)
Actinopterygii sall4 31 30
  • 56.56 (n)
OneToOne
sbcb372 30
fruit fly
(Drosophila melanogaster)
Insecta salr 31
  • 22 (a)
ManyToMany
salm 31
  • 20 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea sem-4 31
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FZF1 31
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 25 (a)
ManyToMany
-- 31
  • 21 (a)
ManyToMany
Species where no ortholog for SALL4 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 SALL4 Gene

ENSEMBL:
Gene Tree for SALL4 (if available)
TreeFam:
Gene Tree for SALL4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SALL4: view image

Paralogs for SALL4 Gene

(13) SIMAP similar genes for SALL4 Gene using alignment to 2 proteins:

  • SALL4_HUMAN
  • Q6Y8G5_HUMAN
genes like me logo Genes that share paralogs with SALL4: view

Variants for SALL4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SALL4 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
3319 Pathogenic: Duane-radial ray syndrome 51,791,428(-) GC/G FRAMESHIFT_VARIANT
3320 Pathogenic: Duane-radial ray syndrome 51,791,541(-) A/AG FRAMESHIFT_VARIANT
3321 Pathogenic: Duane-radial ray syndrome 51,790,578(-) GA/G FRAMESHIFT_VARIANT,INTRON_VARIANT
3323 Pathogenic: Duane-radial ray syndrome 51,790,057(-) GC/G FRAMESHIFT_VARIANT,INTRON_VARIANT
3324 Pathogenic: Duane-radial ray syndrome 51,792,156(-) AG/A FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for SALL4 Gene

Structural Variations from Database of Genomic Variants (DGV) for SALL4 Gene

Variant ID Type Subtype PubMed ID
esv2758800 CNV loss 17122850
nsv964409 CNV duplication 23825009
nsv979442 CNV duplication 23825009

Variation tolerance for SALL4 Gene

Residual Variation Intolerance Score: 16.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.17; 92.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SALL4 Gene

Human Gene Mutation Database (HGMD)
SALL4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SALL4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SALL4 Gene

Disorders for SALL4 Gene

MalaCards: The human disease database

(42) MalaCards diseases for SALL4 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
duane-radial ray syndrome
  • drrs
ivic syndrome
  • radial ray defects, hearing impairment, external ophthalmoplegia, and thrombocytopenia
okihiro syndrome due to a point mutation
  • duane-radial ray syndrome due to a point mutation
okihiro syndrome due to 20q13 microdeletion
  • duane-radial ray syndrome due to monosomy 20q13
duane retraction syndrome
  • drs
- elite association - COSMIC cancer census association via MalaCards
Search SALL4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SALL4_HUMAN
  • Duane-radial ray syndrome (DRRS) [MIM:607323]: Disorder characterized by the association of forearm malformations with Duane retraction syndrome. {ECO:0000269 PubMed:12393809, ECO:0000269 PubMed:12395297, ECO:0000269 PubMed:16402211}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Oculootoradial syndrome (OORS) [MIM:147750]: Autosomal dominant condition characterized by upper limbs anomalies (radial ray defects, carpal bones fusion), extraocular motor disturbances, congenital bilateral non-progressive mixed hearing loss. Other less consistent malformations include heart involvement, mild thrombocytopenia and leukocytosis (before age 50), shoulder girdle hypoplasia, imperforate anus, kidney malrotation or rectovaginal fistula. The IVIC syndrome is an allelic disorder of Duane-radial ray syndrome (DRRS) with a similar phenotype. {ECO:0000269 PubMed:17256792}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SALL4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SALL4: view

No data available for Genatlas for SALL4 Gene

Publications for SALL4 Gene

  1. A SALL4 zinc finger missense mutation predicted to result in increased DNA binding affinity is associated with cranial midline defects and mild features of Okihiro syndrome. (PMID: 16402211) Miertus J … Kohlhase J (Human genetics 2006) 3 4 23 54
  2. Duane radial ray syndrome (Okihiro syndrome) maps to 20q13 and results from mutations in SALL4, a new member of the SAL family. (PMID: 12395297) Al-Baradie R … Engle EC (American journal of human genetics 2002) 3 4 23 54
  3. Sumoylation is important for stability, subcellular localization, and transcriptional activity of SALL4, an essential stem cell transcription factor. (PMID: 23012367) Yang F … Dai W (The Journal of biological chemistry 2012) 3 4 54
  4. A BEN-domain-containing protein associates with heterochromatin and represses transcription. (PMID: 21914818) Sathyan KM … Prasanth SG (Journal of cell science 2011) 3 4 54
  5. 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 41 54

Products for SALL4 Gene

Sources for SALL4 Gene