Human Gene SATB2 (ENST00000260926.9) from GENCODE V44
  Description: Homo sapiens SATB homeobox 2 (SATB2), transcript variant 3, mRNA. (from RefSeq NM_001172517)
RefSeq Summary (NM_001172517): 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 cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010].
Gencode Transcript: ENST00000260926.9
Gencode Gene: ENSG00000119042.18
Transcript (Including UTRs)
   Position: hg38 chr2:199,269,508-199,465,108 Size: 195,601 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr2:199,272,211-199,456,037 Size: 183,827 Coding Exon Count: 10 

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 (chr2:199,269,508-199,465,108)mRNA (may differ from genome)Protein (733 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SATB2_HUMAN
DESCRIPTION: RecName: Full=DNA-binding protein SATB2; AltName: Full=Special AT-rich sequence-binding protein 2;
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.
SUBUNIT: Interacts with ATF4 and RUNX2; resulting in enhanced DNA binding and transactivation by these transcription factors (By similarity). Interacts with PIAS1.
SUBCELLULAR LOCATION: Nucleus matrix.
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.
PTM: Sumoylated by PIAS1. Sumoylation promotes nuclear localization, but represses transcription factor activity.
DISEASE: Note=Chromosomal aberrations involving SATB2 are found in isolated cleft palate. Translocation t(2;7); translocation t(2;11).
DISEASE: Defects in SATB2 are a cause of 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.
DISEASE: Note=A chromosomal aberration involving SATB2 is found in a patient with classical features of Toriello-Carey syndrome. Translocation t(2;14)(q33;q22).
SIMILARITY: Belongs to the CUT homeobox family.
SIMILARITY: Contains 2 CUT DNA-binding domains.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=BAA82986.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

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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: SATB2
Diseases sorted by gene-association score: glass syndrome* (1042), satb2-associated syndrome* (443), cleft palate, isolated (18), eec syndrome (13), periampullary adenocarcinoma (11), acrofrontofacionasal dysostosis (11), adult syndrome (11), periosteal osteogenic sarcoma (11), mucinous ovarian cystadenoma (10), rapp-hodgkin syndrome (9), maxillonasal dysplasia, binder type (9), listeria meningitis (8), physical disorder (8), cleft lip/palate-ectodermal dysplasia syndrome (8), hydrolethalus syndrome (8), syndromic x-linked intellectual disability siderius type (8), conventional central osteosarcoma (8), small cell osteogenic sarcoma (8), 3mc syndrome (7), bone osteosarcoma (7), peripheral osteosarcoma (7), ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 (7), cavernous sinus thrombosis (7), intraocular retinoblastoma (7), juxtacortical osteosarcoma (6), sc phocomelia syndrome (6), popliteal pterygium syndrome 1 (6), meningocele (6), ovarian mucinous neoplasm (6), hemifacial microsomia (6), ladd syndrome (6), van der woude syndrome (6), opitz-gbbb syndrome (5), diaphragmatic eventration (5), cloacal exstrophy (5), orofacial cleft (5), hypoparathyroidism-deafness-renal disease syndrome (5), chromosome 2q35 duplication syndrome (4), thrombocytopenia-absent radius syndrome (4), split-hand/foot malformation 4 (4), osteoporosis (2), tooth agenesis (1)
* = 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: 13.12 RPKM in Colon - Transverse
Total median expression: 74.07 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 -125.90413-0.305 Picture PostScript Text
3' UTR -601.602703-0.223 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
IPR003350 - Hmoeo_CUT
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR010982 - Lambda_DNA-bd_dom

Pfam Domains:
PF02376 - CUT domain
PF00046 - Homeobox domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WI3 - NMR MuPIT 1WIZ - NMR MuPIT 2CSF - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UPW6
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-  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     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
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:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001764 neuron migration
GO:0002076 osteoblast development
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0009880 embryonic pattern specification
GO:0010468 regulation of gene expression
GO:0021902 commitment of neuronal cell to specific neuron type in forebrain
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048704 embryonic skeletal system morphogenesis
GO:0051216 cartilage development
GO:0060021 palate development
GO:0071310 cellular response to organic substance

Cellular Component:
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0016363 nuclear matrix


-  Descriptions from all associated GenBank mRNAs
  LP896215 - Sequence 1079 from Patent EP3253886.
AB028957 - Homo sapiens KIAA1034 mRNA for KIAA1034 protein.
AB209376 - Homo sapiens mRNA for SATB family member 2 variant protein.
AK056638 - Homo sapiens cDNA FLJ32076 fis, clone OCBBF1000153, highly similar to DNA-binding protein SATB2.
BC098136 - Homo sapiens SATB homeobox 2, mRNA (cDNA clone MGC:119475 IMAGE:40007830), complete cds.
BC099723 - Homo sapiens SATB homeobox 2, mRNA (cDNA clone MGC:119477 IMAGE:40007832), complete cds.
BC103492 - Homo sapiens SATB homeobox 2, mRNA (cDNA clone MGC:119474 IMAGE:40007829), complete cds.
BC103500 - Homo sapiens SATB homeobox 2, mRNA (cDNA clone MGC:119476 IMAGE:40007831), complete cds.
AK291463 - Homo sapiens cDNA FLJ77828 complete cds.
AB384088 - Synthetic construct DNA, clone: pF1KSDA1034, Homo sapiens SATB2 gene for DNA-binding protein SATB2, complete cds, without stop codon, in Flexi system.
EU446695 - Synthetic construct Homo sapiens clone IMAGE:100070058; IMAGE:100011904; FLH257182.01L SATB homeobox 2 (SATB2) gene, encodes complete protein.
KJ893357 - Synthetic construct Homo sapiens clone ccsbBroadEn_02751 SATB2 gene, encodes complete protein.
JD486855 - Sequence 467879 from Patent EP1572962.
JD520311 - Sequence 501335 from Patent EP1572962.
JD354687 - Sequence 335711 from Patent EP1572962.
JD280795 - Sequence 261819 from Patent EP1572962.
JD160417 - Sequence 141441 from Patent EP1572962.
JD296813 - Sequence 277837 from Patent EP1572962.
JD267033 - Sequence 248057 from Patent EP1572962.
JD287996 - Sequence 269020 from Patent EP1572962.
JD093759 - Sequence 74783 from Patent EP1572962.
JD360085 - Sequence 341109 from Patent EP1572962.
JD525256 - Sequence 506280 from Patent EP1572962.
JD046952 - Sequence 27976 from Patent EP1572962.
JD052172 - Sequence 33196 from Patent EP1572962.
JD311363 - Sequence 292387 from Patent EP1572962.
JD037878 - Sequence 18902 from Patent EP1572962.
JD036681 - Sequence 17705 from Patent EP1572962.
JD423225 - Sequence 404249 from Patent EP1572962.
JD561152 - Sequence 542176 from Patent EP1572962.
JD298733 - Sequence 279757 from Patent EP1572962.
JD300393 - Sequence 281417 from Patent EP1572962.
JD428760 - Sequence 409784 from Patent EP1572962.
AK025127 - Homo sapiens cDNA: FLJ21474 fis, clone COL04941.
AJ438951 - Homo sapiens mRNA for KIAA1034 gene splice variant, clone ATCC 160988.
JD205491 - Sequence 186515 from Patent EP1572962.

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

Protein Q9UPW6 (Reactome details) participates in the following event(s):

R-HSA-4615900 PIAS1 SUMOylates SATB2 with SUMO3
R-HSA-8985275 RUNX2 binds to SATB2
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-8940973 RUNX2 regulates osteoblast differentiation
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-8941326 RUNX2 regulates bone development
R-HSA-2990846 SUMOylation
R-HSA-8878166 Transcriptional regulation by RUNX2
R-HSA-597592 Post-translational protein modification
R-HSA-212436 Generic Transcription Pathway
R-HSA-392499 Metabolism of proteins
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8K5Z8, ENST00000260926.1, ENST00000260926.2, ENST00000260926.3, ENST00000260926.4, ENST00000260926.5, ENST00000260926.6, ENST00000260926.7, ENST00000260926.8, KIAA1034, NM_001172517, Q4V763, Q9UPW6, SATB2_HUMAN, uc002uva.1, uc002uva.2, uc002uva.3
UCSC ID: ENST00000260926.9
RefSeq Accession: NM_001172517
Protein: Q9UPW6 (aka SATB2_HUMAN or SAB2_HUMAN)
CCDS: CCDS2327.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SATB2:
satb2-dis (SATB2-Associated Syndrome)

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