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Aliases for SALL2 Gene

Aliases for SALL2 Gene

  • Spalt Like Transcription Factor 2 2 3 5
  • Zinc Finger Protein Spalt-2 3 4
  • Zinc Finger Protein SALL2 3 4
  • Zinc Finger Protein 795 3 4
  • ZNF795 3 4
  • Sal-2 3 4
  • Sal (Drosophila)-Like 2 2
  • Sal-Like 2 (Drosophila) 2
  • Sal-Like Protein 2 3
  • P150(Sal2) 3
  • KIAA0360 4
  • HSAL2 3
  • HSal2 4
  • COLB 3
  • SAL2 4

External Ids for SALL2 Gene

Previous GeneCards Identifiers for SALL2 Gene

  • GC14M019361
  • GC14M015776
  • GC14M019979
  • GC14M019980
  • GC14M021059
  • GC14U900549
  • GC14M021989
  • GC14M002107

Summaries for SALL2 Gene

Entrez Gene Summary for SALL2 Gene

  • This gene encodes a protein containing multiple zinc finger domains. The encoded protein functions in optical fissure closure during development of the eye in the embryo. Mutations in this gene are associated with ocular coloboma. [provided by RefSeq, Jul 2016]

GeneCards Summary for SALL2 Gene

SALL2 (Spalt Like Transcription Factor 2) is a Protein Coding gene. Diseases associated with SALL2 include Coloboma, Ocular, Autosomal Recessive and Coloboma Of Eyelid. An important paralog of this gene is SALL3.

UniProtKB/Swiss-Prot for SALL2 Gene

  • Probable transcription factor that plays a role in eye development before, during, and after optic fissure closure.

Gene Wiki entry for SALL2 Gene

Additional gene information for SALL2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SALL2 Gene

Genomics for SALL2 Gene

GeneHancer (GH) Regulatory Elements for SALL2 Gene

Promoters and enhancers for SALL2 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
GH14J021524 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 658.2 +9.7 9700 5.2 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF143 SP3 SALL2 METTL17 METTL3 SUPT16H CHD8 ENSG00000257096
GH14J021533 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.7 1695 4.9 ZNF768 USF1 FOXA2 SIN3A ZMYM3 EBF1 ZIC2 ZNF48 ETS1 FOXK2 SALL2 ENSG00000257096
GH14J021538 Enhancer 0.4 ENCODE dbSUPER 650.7 -2.0 -1958 1.9 SALL2 RBBP4P5
GH14J021555 Enhancer 1.4 Ensembl ENCODE dbSUPER 18.4 -20.0 -20035 3.5 FOXA2 ARID4B SIN3A ZNF2 ZNF48 ETS1 YY1 SLC30A9 ZNF121 ARID2 SALL2 ENSG00000257096 SNORD8 UBA52P2 SNORD9 RPGRIP1 RBBP4P5
GH14J021454 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.6 +81.2 81209 2.9 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARID4B SIN3A DMAP1 YY1 POLR2B HNRNPC CHD8 SUPT16H PNP METTL3 UBA52P2 SNORD8 SNORD9 ENSG00000257096 SALL2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SALL2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SALL2 gene promoter:
  • AREB6
  • RREB-1
  • NF-kappaB2
  • NF-kappaB1
  • NF-kappaB
  • MyoD
  • GR
  • GR-alpha
  • AML1a
  • PPAR-gamma2

Genomic Locations for SALL2 Gene

Genomic Locations for SALL2 Gene
16,137 bases
Minus strand
16,120 bases
Minus strand

Genomic View for SALL2 Gene

Genes around SALL2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SALL2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SALL2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SALL2 Gene

Proteins for SALL2 Gene

  • Protein details for SALL2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sal-like protein 2
    Protein Accession:
    Secondary Accessions:
    • B2RMX6
    • B9EGK8
    • Q8N656
    • Q9Y4G1

    Protein attributes for SALL2 Gene

    1007 amino acids
    Molecular mass:
    105309 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA21638.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for SALL2 Gene


neXtProt entry for SALL2 Gene

Post-translational modifications for SALL2 Gene

  • Ubiquitination at posLast=911911
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SALL2 Gene

Domains & Families for SALL2 Gene

Gene Families for SALL2 Gene

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

Protein Domains for SALL2 Gene


Suggested Antigen Peptide Sequences for SALL2 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 SALL2: view

Function for SALL2 Gene

Molecular function for SALL2 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription factor that plays a role in eye development before, during, and after optic fissure closure.
GENATLAS Biochemistry:
brain specific transcription factor,Drosophila homeotic gene Sal-like 2,expressed in different brain areas

Phenotypes From GWAS Catalog for SALL2 Gene

Gene Ontology (GO) - Molecular Function for SALL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 21362508
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP 21362508
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with SALL2: view
genes like me logo Genes that share phenotypes with SALL2: view

Human Phenotype Ontology for SALL2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SALL2 Gene

MGI Knock Outs for SALL2:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SALL2 Gene

Localization for SALL2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SALL2 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 SALL2 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SALL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0016581 NuRD complex IEA --
genes like me logo Genes that share ontologies with SALL2: view

Pathways & Interactions for SALL2 Gene

SuperPathways for SALL2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SALL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA --
GO:0001654 eye development IDA 24412933
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA,IBA --
GO:0006366 transcription by RNA polymerase II IBA --
genes like me logo Genes that share ontologies with SALL2: view

No data available for Pathways by source and SIGNOR curated interactions for SALL2 Gene

Drugs & Compounds for SALL2 Gene

No Compound Related Data Available

Transcripts for SALL2 Gene

mRNA/cDNA for SALL2 Gene

(5) REFSEQ mRNAs :
(13) Additional mRNA sequences :
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SALL2 Gene

Sal-like 2 (Drosophila):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SALL2 Gene

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

Relevant External Links for SALL2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SALL2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SALL2 Gene

mRNA differential expression in normal tissues according to GTEx for SALL2 Gene

This gene is overexpressed in Brain - Cerebellum (x5.5) and Brain - Cerebellar Hemisphere (x5.1).

Protein differential expression in normal tissues from HIPED for SALL2 Gene

This gene is overexpressed in Plasma (45.8) and Adipocyte (22.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SALL2 Gene

Protein tissue co-expression partners for SALL2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SALL2 Gene:


SOURCE GeneReport for Unigene cluster for SALL2 Gene:


mRNA Expression by UniProt/SwissProt for SALL2 Gene:

Tissue specificity: Highest levels in adult brain (in different areas). Lower levels in heart; very low levels in kidney and pancreas. Expressed throughout the retina and lens vesicle as well as the periocular mesenchyme.

Evidence on tissue expression from TISSUES for SALL2 Gene

  • Nervous system(4.9)
  • Liver(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SALL2 Gene

Germ Layers:
  • ectoderm
  • nervous
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • peripheral nervous system
genes like me logo Genes that share expression patterns with SALL2: view

Orthologs for SALL2 Gene

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

Orthologs for SALL2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SALL2 34 33
  • 99.64 (n)
(Mus musculus)
Mammalia Sall2 16 34 33
  • 85.96 (n)
(Rattus norvegicus)
Mammalia Sall2 33
  • 85.82 (n)
(Monodelphis domestica)
Mammalia SALL2 34
  • 80 (a)
(Canis familiaris)
Mammalia SALL2 34
  • 70 (a)
(Anolis carolinensis)
Reptilia SALL2 34
  • 60 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sall2 33
  • 58.76 (n)
(Danio rerio)
Actinopterygii SALL2 34
  • 23 (a)
fruit fly
(Drosophila melanogaster)
Insecta salr 34
  • 15 (a)
salm 34 35
  • 15 (a)
(Caenorhabditis elegans)
Secernentea sem-4 34
  • 15 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FZF1 34
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 16 (a)
-- 34
  • 15 (a)
Species where no ortholog for SALL2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 SALL2 Gene

Gene Tree for SALL2 (if available)
Gene Tree for SALL2 (if available)
Evolutionary constrained regions (ECRs) for SALL2: view image

Paralogs for SALL2 Gene

Paralogs for SALL2 Gene

(20) SIMAP similar genes for SALL2 Gene using alignment to 7 proteins:

  • E7EW59_HUMAN
  • F5GY43_HUMAN
  • F5H1G6_HUMAN
  • F5H433_HUMAN
  • Q8N656_HUMAN
genes like me logo Genes that share paralogs with SALL2: view

Variants for SALL2 Gene

Sequence variations from dbSNP and Humsavar for SALL2 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs587776429 pathogenic, Ocular coloboma, autosomal recessive 21,525,643(-) C/A coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs1000192551 -- 21,522,316(-) C/G 3_prime_UTR_variant, intron_variant
rs1000238765 -- 21,534,851(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000251001 -- 21,529,153(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000303361 -- 21,528,739(-) C/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SALL2 Gene

Variant ID Type Subtype PubMed ID
esv2422459 CNV duplication 17116639
esv2660046 CNV deletion 23128226
esv3633716 CNV gain 21293372
esv3633718 CNV gain 21293372
nsv1071137 CNV deletion 25765185
nsv472468 CNV novel sequence insertion 20440878
nsv522850 CNV gain 19592680

Variation tolerance for SALL2 Gene

Residual Variation Intolerance Score: 16.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.78; 89.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SALL2 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SALL2 Gene

Disorders for SALL2 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SALL2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
coloboma, ocular, autosomal recessive
  • coar
coloboma of eyelid
coloboma of eye lens
coloboma of optic nerve
  • morning glory disc anomaly
coloboma of macula
  • agenesis of macula
- elite association - COSMIC cancer census association via MalaCards
Search SALL2 in MalaCards View complete list of genes associated with diseases


  • Coloboma, ocular, autosomal recessive (COAR) [MIM:216820]: An ocular anomaly resulting from abnormal morphogenesis of the optic cup and stalk, and incomplete fusion of the fetal intra-ocular fissure during gestation. The clinical presentation is variable. Some individuals may present with minimal defects in the anterior iris leaf without other ocular defects. More complex malformations create a combination of iris, uveoretinal and/or optic nerve defects without or with microphthalmia or even anophthalmia. {ECO:0000269 PubMed:24412933}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SALL2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SALL2: view

No data available for Genatlas for SALL2 Gene

Publications for SALL2 Gene

  1. Isolation, characterization, and organ-specific expression of two novel human zinc finger genes related to the Drosophila gene spalt. (PMID: 8975705) Kohlhase J … Stick R (Genomics 1996) 2 3 4 58
  2. Mutation of SALL2 causes recessive ocular coloboma in humans and mice. (PMID: 24412933) Kelberman D … Sowden JC (Human molecular genetics 2014) 3 4 58
  3. 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
  4. Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. (PMID: 14507652) Nielsen TO … van de Rijn M (The American journal of pathology 2003) 3 22 58
  5. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D … Nagase T (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4 58

Products for SALL2 Gene

Sources for SALL2 Gene

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