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Aliases for SATB2 Gene

Aliases for SATB2 Gene

  • SATB Homeobox 2 2 3 5
  • Special AT-Rich Sequence-Binding Protein 2 3 4
  • SATB Family Member 2 2 3
  • DNA-Binding Protein SATB2 3
  • KIAA1034 4
  • GLSS 3

External Ids for SATB2 Gene

Previous GeneCards Identifiers for SATB2 Gene

  • GC02M200098
  • GC02M200336
  • GC02M199959
  • GC02M199842
  • GC02M191986

Summaries for SATB2 Gene

Entrez Gene Summary for SATB2 Gene

  • This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and mental retardation. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]

GeneCards Summary for SATB2 Gene

SATB2 (SATB Homeobox 2) is a Protein Coding gene. Diseases associated with SATB2 include Glass Syndrome and Satb2-Associated Syndrome. GO annotations related to this gene include sequence-specific DNA binding and chromatin binding. An important paralog of this gene is SATB1.

UniProtKB/Swiss-Prot for SATB2 Gene

  • Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Required for the initiation of the upper-layer neurons (UL1) specific genetic program and for the inactivation of deep-layer neurons (DL) and UL2 specific genes, probably by modulating BCL11B expression. Repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex. May play an important role in palate formation. Acts as a molecular node in a transcriptional network regulating skeletal development and osteoblast differentiation.

Gene Wiki entry for SATB2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SATB2 Gene

Genomics for SATB2 Gene

Regulatory Elements for SATB2 Gene

Enhancers for SATB2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G198967 1.6 ENCODE 16.9 +503.1 503089 2.3 ZNF263 GATA3 ZNF341 FEZF1 ATF2 TCF7L2 SATB2 GC02M198975 GC02P198955
GH02G199430 1.4 Ensembl ENCODE dbSUPER 12.5 +38.6 38643 3.4 PKNOX1 FEZF1 ETS1 TCF12 GATA2 FOS ZNF362 ZEB2 ZNF843 ZNF592 SATB2 SPATS2L SATB2-AS1 GC02M199366
GH02G199302 1.2 FANTOM5 Ensembl ENCODE dbSUPER 11.9 +167.5 167549 2.5 BHLHE40 FOS ENSG00000257045 SATB2 GC02P199311 GC02M199231
GH02G199454 2 FANTOM5 Ensembl ENCODE dbSUPER 7.1 +12.0 11982 10.3 MLX AGO1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TYW5 SATB2 SATB2-AS1
GH02G199442 1.1 dbSUPER 11.6 +29.1 29139 1.3 FOXA2 PKNOX1 ARNT MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SATB2 SATB2-AS1 GC02M199366
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SATB2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SATB2 Gene

Chromosome:
2
Start:
199,269,500 bp from pter
End:
199,471,266 bp from pter
Size:
201,767 bases
Orientation:
Minus strand

Genomic View for SATB2 Gene

Genes around SATB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SATB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SATB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SATB2 Gene

Proteins for SATB2 Gene

  • Protein details for SATB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPW6-SATB2_HUMAN
    Recommended name:
    DNA-binding protein SATB2
    Protein Accession:
    Q9UPW6
    Secondary Accessions:
    • A8K5Z8
    • Q3ZB87
    • Q4V763

    Protein attributes for SATB2 Gene

    Size:
    733 amino acids
    Molecular mass:
    82555 Da
    Quaternary structure:
    • Interacts with ATF4 and RUNX2; resulting in enhanced DNA binding and transactivation by these transcription factors (By similarity). Interacts with PIAS1.
    SequenceCaution:
    • Sequence=BAA82986.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SATB2 Gene

    Alternative splice isoforms for SATB2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SATB2 Gene

Post-translational modifications for SATB2 Gene

  • Sumoylated by PIAS1. Sumoylation promotes nuclear localization, but represses transcription factor activity.
  • Ubiquitination at Lys184
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for SATB2

No data available for DME Specific Peptides for SATB2 Gene

Domains & Families for SATB2 Gene

Gene Families for SATB2 Gene

Protein Domains for SATB2 Gene

Suggested Antigen Peptide Sequences for SATB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UPW6

UniProtKB/Swiss-Prot:

SATB2_HUMAN :
  • Belongs to the CUT homeobox family.
Family:
  • Belongs to the CUT homeobox family.
genes like me logo Genes that share domains with SATB2: view

Function for SATB2 Gene

Molecular function for SATB2 Gene

UniProtKB/Swiss-Prot Function:
Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Required for the initiation of the upper-layer neurons (UL1) specific genetic program and for the inactivation of deep-layer neurons (DL) and UL2 specific genes, probably by modulating BCL11B expression. Repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex. May play an important role in palate formation. Acts as a molecular node in a transcriptional network regulating skeletal development and osteoblast differentiation.

Gene Ontology (GO) - Molecular Function for SATB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 20829881
genes like me logo Genes that share ontologies with SATB2: view
genes like me logo Genes that share phenotypes with SATB2: view

Human Phenotype Ontology for SATB2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SATB2 Gene

MGI Knock Outs for SATB2:

Animal Model Products

CRISPR Products

miRNA for SATB2 Gene

miRTarBase miRNAs that target SATB2

Inhibitory RNA Products

Cell Line Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SATB2 Gene

Localization for SATB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SATB2 Gene

Nucleus matrix.

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 SATB2 gene
Compartment Confidence
nucleus 5
plasma membrane 2
cytosol 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SATB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex IEA --
GO:0005634 nucleus IBA,IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005667 transcription factor complex IEA --
GO:0016363 nuclear matrix IEA --
genes like me logo Genes that share ontologies with SATB2: view

Pathways & Interactions for SATB2 Gene

SuperPathways for SATB2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SATB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001764 neuron migration IEA --
GO:0002076 osteoblast development IEA --
GO:0006338 chromatin remodeling IEA --
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with SATB2: view

No data available for Pathways by source and SIGNOR curated interactions for SATB2 Gene

Transcripts for SATB2 Gene

Unigene Clusters for SATB2 Gene

SATB homeobox 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SATB2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
SP1: - - -
SP2: - -
SP3: - - - - -
SP4: -
SP5: -
SP6:

Relevant External Links for SATB2 Gene

GeneLoc Exon Structure for
SATB2
ECgene alternative splicing isoforms for
SATB2

Expression for SATB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SATB2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SATB2 Gene

This gene is overexpressed in Colon - Transverse (x8.6), Brain - Frontal Cortex (BA9) (x5.6), Brain - Anterior cingulate cortex (BA24) (x4.2), and Brain - Cortex (x4.1).

Protein differential expression in normal tissues from HIPED for SATB2 Gene

This gene is overexpressed in Colon (26.1), Heart (20.1), Fetal Brain (12.1), and Rectum (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SATB2 Gene



Protein tissue co-expression partners for SATB2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SATB2 Gene:

SATB2

SOURCE GeneReport for Unigene cluster for SATB2 Gene:

Hs.516617

mRNA Expression by UniProt/SwissProt for SATB2 Gene:

Q9UPW6-SATB2_HUMAN
Tissue specificity: High expression in adult brain, moderate expression in fetal brain, and weak expression in adult liver, kidney, and spinal cord and in select brain regions, including amygdala, corpus callosum, caudate nucleus, and hippocampus.

Evidence on tissue expression from TISSUES for SATB2 Gene

  • Nervous system(4.9)
  • Intestine(2.7)
  • Bone(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SATB2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • skull
  • tooth
Abdomen:
  • abdominal wall
  • intestine
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with SATB2: view

Primer Products

Orthologs for SATB2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SATB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SATB2 34 35
  • 99.68 (n)
oppossum
(Monodelphis domestica)
Mammalia SATB2 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SATB2 34 35
  • 95.54 (n)
cow
(Bos Taurus)
Mammalia SATB2 34 35
  • 94.04 (n)
mouse
(Mus musculus)
Mammalia Satb2 34 16 35
  • 92.41 (n)
rat
(Rattus norvegicus)
Mammalia Satb2 34
  • 91.72 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SATB2 35
  • 91 (a)
OneToOne
chicken
(Gallus gallus)
Aves SATB2 34 35
  • 87.37 (n)
lizard
(Anolis carolinensis)
Reptilia SATB2 35
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia satb2 34
  • 77.69 (n)
zebrafish
(Danio rerio)
Actinopterygii satb2 34 35
  • 70.78 (n)
Species where no ortholog for SATB2 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SATB2 Gene

ENSEMBL:
Gene Tree for SATB2 (if available)
TreeFam:
Gene Tree for SATB2 (if available)

Paralogs for SATB2 Gene

Paralogs for SATB2 Gene

(1) SIMAP similar genes for SATB2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SATB2: view

Variants for SATB2 Gene

Sequence variations from dbSNP and Humsavar for SATB2 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1057518190 Pathogenic 199,328,888(-) TCTGC(A/G)TAAGG reference, missense
rs1057518496 Pathogenic 199,349,006(-) CATTA(C/T)AGCCC reference, stop-gained
rs1057518614 Pathogenic 199,272,470(-) ACACT(-/CT)TTCGG reference, frameshift-variant
rs137853127 Pathogenic 199,349,159(-) TGGAA(C/T)GAGAA reference, stop-gained
rs797044874 Pathogenic 199,349,027(-) CAATC(C/T)GAAAC reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for SATB2 Gene

Variant ID Type Subtype PubMed ID
dgv2127n106 CNV deletion 24896259
esv1009594 CNV deletion 20482838
esv2110977 CNV deletion 18987734
esv2572304 CNV deletion 19546169
esv2661101 CNV deletion 23128226
esv2670764 CNV deletion 23128226
esv2721352 CNV deletion 23290073
esv2721353 CNV deletion 23290073
esv27345 CNV loss 19812545
esv3560807 CNV deletion 23714750
esv3584268 CNV loss 25503493
esv3584269 CNV loss 25503493
esv3593941 CNV loss 21293372
esv3593942 CNV gain 21293372
esv3593943 CNV loss 21293372
esv3593944 CNV loss 21293372
esv3593945 CNV loss 21293372
esv3593946 CNV loss 21293372
esv4682 CNV loss 18987735
esv7603 CNV loss 19470904
esv993308 CNV deletion 20482838
nsv1073004 CNV deletion 25765185
nsv1149651 CNV deletion 26484159
nsv213912 CNV deletion 16902084
nsv3104 CNV insertion 18451855
nsv441800 CNV loss 18776908
nsv514113 CNV loss 21397061
nsv955060 CNV deletion 24416366

Variation tolerance for SATB2 Gene

Residual Variation Intolerance Score: 5.29% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.65; 13.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SATB2 Gene

Human Gene Mutation Database (HGMD)
SATB2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SATB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SATB2 Gene

Disorders for SATB2 Gene

MalaCards: The human disease database

(47) MalaCards diseases for SATB2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
glass syndrome
  • chromosome 2q32-q33 deletion syndrome
satb2-associated syndrome
  • glass syndrome
physical disorder
  • physical illness
acrofrontofacionasal dysostosis
  • affn dysostosis
periosteal osteogenic sarcoma
  • parosteal osteosarcoma
- elite association - COSMIC cancer census association via MalaCards
Search SATB2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SATB2_HUMAN
  • Cleft palate isolated (CPI) [MIM:119540]: A congenital fissure of the soft and/or hard palate, due to faulty fusion. Isolated cleft palate is not associated with cleft lips. Some patients may manifest other craniofacial dysmorphic features, mental retardation, and osteoporosis. {ECO:0000269 PubMed:12915443, ECO:0000269 PubMed:17377962}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving SATB2 is found in a patient with classical features of Toriello-Carey syndrome. Translocation t(2;14)(q33;q22). {ECO:0000269 PubMed:19170718}.
  • Note=Chromosomal aberrations involving SATB2 are found in isolated cleft palate. Translocation t(2;7); translocation t(2;11). {ECO:0000269 PubMed:12915443}.

Relevant External Links for SATB2

Genetic Association Database (GAD)
SATB2
Human Genome Epidemiology (HuGE) Navigator
SATB2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SATB2
genes like me logo Genes that share disorders with SATB2: view

No data available for Genatlas for SATB2 Gene

Publications for SATB2 Gene

  1. Identification of SATB2 as the cleft palate gene on 2q32-q33. (PMID: 12915443) FitzPatrick D.R. … Bonthron D.T. (Hum. Mol. Genet. 2003) 3 4 22 64
  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 J.C. (PLoS ONE 2010) 3 46 64
  3. Testing reported associations of genetic risk factors for oral clefts in a large Irish study population. (PMID: 19937600) Carter T.C. … Mills J.L. (Birth Defects Res. Part A Clin. Mol. Teratol. 2010) 3 46 64
  4. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. (PMID: 20228799) McGovern D.P. … Seielstad M. (Nat. Genet. 2010) 3 46 64
  5. Toriello-Carey syndrome in a patient with a de novo balanced translocation [46,XY,t(2;14)(q33;q22)] interrupting SATB2. (PMID: 19170718) Tegay D.H. … Hatchwell E. (Clin. Genet. 2009) 4 22 64

Products for SATB2 Gene

Sources for SATB2 Gene

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