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SATB2 SATB homeobox 2 [ Homo sapiens (human) ]

Gene ID: 23314, updated on 2-Nov-2024

Summary

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Official Symbol
SATB2provided by HGNC
Official Full Name
SATB homeobox 2provided by HGNC
Primary source
HGNC:HGNC:21637
See related
Ensembl:ENSG00000119042 MIM:608148; AllianceGenome:HGNC:21637
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GLSS; DEL2Q32Q33; C2DELq32q33
Summary
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]
Expression
Biased expression in colon (RPKM 13.7), brain (RPKM 6.3) and 7 other tissues See more
Orthologs
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Genomic context

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See SATB2 in Genome Data Viewer
Location:
2q33.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (199269500..199471266, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (199753552..199955035, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (200134223..200335989, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene MIA SH3 domain ER export factor 2 pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:200043891-200044479 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:200049723-200050231 Neighboring gene RNA, U7 small nuclear 147 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr2:200116810-200117393 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:200136608-200137807 Neighboring gene NANOG hESC enhancer GRCh37_chr2:200288662-200289237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12219 Neighboring gene Sharpr-MPRA regulatory region 6083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:200327038-200327803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12220 Neighboring gene SATB2 antisense RNA 1 Neighboring gene long intergenic non-protein coding RNA 1877 Neighboring gene selenophosphate synthetase 1 pseudogene 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pathogenic SATB2 missense variants affecting p.Gly392 have variable functional implications and result in diverse clinical phenotypes.
    Title: Pathogenic SATB2 missense variants affecting p.Gly392 have variable functional implications and result in diverse clinical phenotypes.
  2. SATB2 Cytoplasmic Expression is Characteristic of a Subset of Ovarian Stromal Cells and Sex Cord Stromal Tumors.
    Title: SATB2 Cytoplasmic Expression is Characteristic of a Subset of Ovarian Stromal Cells and Sex Cord Stromal Tumors.
  3. Concomitant expression patterns of CDX2 and SATB2 as prognostic factors in stage III colorectal cancers.
    Title: Concomitant expression patterns of CDX2 and SATB2 as prognostic factors in stage III colorectal cancers.
  4. SATB2 organizes the 3D genome architecture of cognition in cortical neurons.
    Title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons.
  5. Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1.
    Title: Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1.
  6. Progress of epigenetic modification of SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate.
    Title: Progress of epigenetic modification of SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate.
  7. Single-cell sequencing reveals SATB2/NOTCH1 signaling promotes the progression of malignancy of epithelial cells from papillary thyroid cancer.
    Title: Single-cell sequencing reveals SATB2/NOTCH1 signaling promotes the progression of malignancy of epithelial cells from papillary thyroid cancer.
  8. Evaluation of Lineage/Site-specific Nuclear Immunohistochemical Markers SATB2, Cyclin D1, SALL4, and BCOR in High-grade Endometrial Carcinomas.
    Title: Evaluation of Lineage/Site-specific Nuclear Immunohistochemical Markers SATB2, Cyclin D1, SALL4, and BCOR in High-grade Endometrial Carcinomas.
  9. microRNA-660 Enhances Cisplatin Sensitivity via Decreasing SATB2 Expression in Lung Adenocarcinoma.
    Title: microRNA-660 Enhances Cisplatin Sensitivity via Decreasing SATB2 Expression in Lung Adenocarcinoma.
  10. YAP-Activated SATB2 Is a Coactivator of NRF2 That Amplifies Antioxidative Capacity and Promotes Tumor Progression in Renal Cell Carcinoma.
    Title: YAP-Activated SATB2 Is a Coactivator of NRF2 That Amplifies Antioxidative Capacity and Promotes Tumor Progression in Renal Cell Carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (135)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Chromosome 2q32-q33 deletion syndrome
MedGen: C2676739 OMIM: 612313 GeneReviews: SATB2-Associated Syndrome
not available

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-07-15)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-15)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study of sleep habits and insomnia.
EBI GWAS Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
EBI GWAS Catalog
Genome-wide association of body fat distribution in African ancestry populations suggests new loci.
EBI GWAS Catalog
Integrative genome-wide association analysis of cytoarchitectural abnormalities in the prefrontal cortex of psychiatric disorders.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection downregulates SATB2 expression in CEM*174 cells and mixed PBMC from HIV infected patients PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21474, FLJ32076, KIAA1034, MGC119474, MGC119477

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables histone deacetylase binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cartilage development IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in embryonic pattern specification IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
  
involved_in osteoblast development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
part_of histone deacetylase complex IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear matrix IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
DNA-binding protein SATB2
Names
SATB family member 2
SATB2 fusion
special AT-rich sequence-binding protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016976.2 RefSeqGene

    Range
    18328..206762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001172509.2 → NP_001165980.1  DNA-binding protein SATB2

    See identical proteins and their annotated locations for NP_001165980.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC016746, AK056638
    Consensus CDS
    CCDS2327.1
    UniProtKB/Swiss-Prot
    A8K5Z8, Q3ZB87, Q4V763, Q9UPW6
    UniProtKB/TrEMBL
    B3KPQ9
    Related
    ENSP00000401112.1, ENST00000417098.6
    Conserved Domains (4) summary
    smart00389
    Location:614 → 671
    HOX; Homeodomain
    cd11585
    Location:60 → 155
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:477 → 556
    CUT; CUT domain
    pfam16557
    Location:162 → 232
    CUTL; CUT1-like DNA-binding domain of SATB

  2. NM_001172517.1 → NP_001165988.1  DNA-binding protein SATB2

    See identical proteins and their annotated locations for NP_001165988.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AB209376, AC016746
    Consensus CDS
    CCDS2327.1
    UniProtKB/Swiss-Prot
    A8K5Z8, Q3ZB87, Q4V763, Q9UPW6
    UniProtKB/TrEMBL
    B3KPQ9
    Related
    ENSP00000260926.5, ENST00000260926.9
    Conserved Domains (4) summary
    smart00389
    Location:614 → 671
    HOX; Homeodomain
    cd11585
    Location:60 → 155
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:477 → 556
    CUT; CUT domain
    pfam16557
    Location:162 → 232
    CUTL; CUT1-like DNA-binding domain of SATB

  3. NM_015265.4 → NP_056080.1  DNA-binding protein SATB2

    See identical proteins and their annotated locations for NP_056080.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC016746, AK291463
    Consensus CDS
    CCDS2327.1
    UniProtKB/Swiss-Prot
    A8K5Z8, Q3ZB87, Q4V763, Q9UPW6
    UniProtKB/TrEMBL
    B3KPQ9
    Related
    ENSP00000405420.1, ENST00000457245.5
    Conserved Domains (4) summary
    smart00389
    Location:614 → 671
    HOX; Homeodomain
    cd11585
    Location:60 → 155
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:477 → 556
    CUT; CUT domain
    pfam16557
    Location:162 → 232
    CUTL; CUT1-like DNA-binding domain of SATB

RNA

  1. NR_134967.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC016746, AJ438951, AK056638
    Related
    ENST00000440919.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    199269500..199471266 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246396.4 → XP_005246453.1  DNA-binding protein SATB2 isoform X2

    UniProtKB/TrEMBL
    B3KPQ9
    Conserved Domains (4) summary
    smart00389
    Location:556 → 613
    HOX; Homeodomain
    cd11585
    Location:2 → 97
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:419 → 497
    CUT; CUT domain
    pfam16557
    Location:128 → 175
    CUTL; CUT1-like DNA-binding domain of SATB

  2. XM_047443775.1 → XP_047299731.1  DNA-binding protein SATB2 isoform X1

    UniProtKB/Swiss-Prot
    A8K5Z8, Q3ZB87, Q4V763, Q9UPW6
    Related
    ENSP00000514854.1, ENST00000700193.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    199753552..199955035 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341120.1 → XP_054197095.1  DNA-binding protein SATB2 isoform X1

    UniProtKB/Swiss-Prot
    A8K5Z8, Q3ZB87, Q4V763, Q9UPW6

  2. XM_054341121.1 → XP_054197096.1  DNA-binding protein SATB2 isoform X2

  3. XM_054341122.1 → XP_054197097.1  DNA-binding protein SATB2 isoform X3

  4. XM_054341123.1 → XP_054197098.1  DNA-binding protein SATB2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UPW6.2 GenPept UniProtKB/Swiss-Prot:Q9UPW6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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