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SATB1 SATB homeobox 1 [ Homo sapiens (human) ]

Gene ID: 6304, updated on 8-Apr-2024

Summary

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Official Symbol
SATB1provided by HGNC
Official Full Name
SATB homeobox 1provided by HGNC
Primary source
HGNC:HGNC:10541
See related
Ensembl:ENSG00000182568 MIM:602075; AllianceGenome:HGNC:10541
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
DEFDA; DHDBV; KTZSL
Summary
This gene encodes a matrix protein which binds nuclear matrix and scaffold-associating DNAs through a unique nuclear architecture. The protein recruits chromatin-remodeling factors in order to regulate chromatin structure and gene expression. [provided by RefSeq, Apr 2016]
Expression
Ubiquitous expression in brain (RPKM 10.9), lymph node (RPKM 7.3) and 25 other tissues See more
Orthologs
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Genomic context

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See SATB1 in Genome Data Viewer
Location:
3p24.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (18345377..18445592, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (18347503..18447703, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (18386869..18487084, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5433 Neighboring gene PDCL3 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:18088671-18088844 Neighboring gene B-cell acute lymphoblastic leukemia associated long RNA 6 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:18140124-18141323 Neighboring gene VISTA enhancer hs250 Neighboring gene uncharacterized LOC124909351 Neighboring gene Sharpr-MPRA regulatory region 1190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:18372491-18373060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:18371920-18372490 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:18386263-18386883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14129 Neighboring gene SATB1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:18557262-18557786 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:18557787-18558309 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:18617865-18619064 Neighboring gene RAD23B pseudogene 1 Neighboring gene RNA, U6 small nuclear 138, pseudogene

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
  • 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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Related articles in PubMed

  1. Overexpression of SATB1 correlates with epithelial-mesenchymal transition and lymphatic metastasis in gastric cancer. Xiao T, et al. Ann Diagn Pathol, 2023 Feb. PMID 36495733
  2. The 3D enhancer network of the developing T cell genome is shaped by SATB1. Zelenka T, et al. Nat Commun, 2022 Nov 14. PMID 36376298, Free PMC Article
  3. [Exploring new molecules that regulate hematopoietic stem cells and early stages of lymphoid hematopoiesis: the functional significance of ESAM and SATB1]. Yokota T. Rinsho Ketsueki, 2022. PMID 36058862
  4. Downregulation of SATB1 by miRNAs reduces megakaryocyte/erythroid progenitor expansion in preclinical models of Diamond-Blackfan anemia. Wilkes MC, et al. Exp Hematol, 2022 Jul. PMID 35460833, Free PMC Article
  5. Elevated Expression of SATB1 Predicts Unfavorable Clinical Outcomes in Colon Adenocarcinoma. Li Y, et al. Appl Immunohistochem Mol Morphol, 2022 May-Jun 01. PMID 35353722

See all (216) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SATB1 mediated tumor colonization and beta-catenin nuclear localization are associated with colorectal cancer progression.
    Title: SATB1 mediated tumor colonization and β-catenin nuclear localization are associated with colorectal cancer progression.
  2. TOX, TWIST1, STAT4, and SATB1 protein expressions in early-stage mycosis fungoides.
    Title: TOX, TWIST1, STAT4, and SATB1 protein expressions in early-stage mycosis fungoides.
  3. Long non-coding RNA LINC00491 accelerates head and neck squamous cell carcinoma progression through regulating miR-508-3p/SATB1 axis and activating Wnt signaling pathway.
    Title: Long non-coding RNA LINC00491 accelerates head and neck squamous cell carcinoma progression through regulating miR-508-3p/SATB1 axis and activating Wnt signaling pathway.
  4. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.
    Title: SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.
  5. SATB1 Chromatin Loops Regulate Megakaryocyte/Erythroid Progenitor Expansion by Facilitating HSP70 and GATA1 Induction.
    Title: SATB1 Chromatin Loops Regulate Megakaryocyte/Erythroid Progenitor Expansion by Facilitating HSP70 and GATA1 Induction.
  6. Overexpression of SATB1 correlates with epithelial-mesenchymal transition and lymphatic metastasis in gastric cancer.
    Title: Overexpression of SATB1 correlates with epithelial-mesenchymal transition and lymphatic metastasis in gastric cancer.
  7. Machine learning links different gene patterns of viral infection to immunosuppression and immune-related biomarkers in severe burns.
    Title: Machine learning links different gene patterns of viral infection to immunosuppression and immune-related biomarkers in severe burns.
  8. The 3D enhancer network of the developing T cell genome is shaped by SATB1.
    Title: The 3D enhancer network of the developing T cell genome is shaped by SATB1.
  9. [Exploring new molecules that regulate hematopoietic stem cells and early stages of lymphoid hematopoiesis: the functional significance of ESAM and SATB1].
    Title: [Exploring new molecules that regulate hematopoietic stem cells and early stages of lymphoid hematopoiesis: the functional significance of ESAM and SATB1].
  10. Downregulation of SATB1 by miRNAs reduces megakaryocyte/erythroid progenitor expansion in preclinical models of Diamond-Blackfan anemia.
    Title: Downregulation of SATB1 by miRNAs reduces megakaryocyte/erythroid progenitor expansion in preclinical models of Diamond-Blackfan anemia.
Submit: New GeneRIF Correction See all GeneRIFs (170)

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
Developmental delay with dysmorphic facies and dental anomalies
MedGen: C5543197 OMIM: 619228 GeneReviews: Not available
Compare labs
Kohlschutter-Tonz syndrome-like
MedGen: C5543202 OMIM: 619229 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog
Susceptibility to chronic mucus hypersecretion, a genome wide association study.
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)

Genotypes

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
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 double-stranded DNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin organization TAS
Traceable Author Statement
more info
 PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in PML body IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA-binding protein SATB1
Names
special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_027814.2 RefSeqGene

    Range
    25250..105212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001131010.4 → NP_001124482.1  DNA-binding protein SATB1 isoform 1

    See identical proteins and their annotated locations for NP_001124482.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, compared to variant 3. Isoform 1 has a shorter C-terminus, compared to isoform 2.
    Source sequence(s)
    AA001621, AC139618, AK127242, BC001744, DA938384, DB141938, DB347409
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    B3KXF1, C9JTR6, Q01826, Q59EQ0
    Related
    ENSP00000399708.2, ENST00000454909.6
    Conserved Domains (4) summary
    smart00389
    Location:644 → 701
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  2. NM_001195470.3 → NP_001182399.1  DNA-binding protein SATB1 isoform 2

    See identical proteins and their annotated locations for NP_001182399.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AA001621, AB209761, AC139618, AC144521, AK127242, DA938384
    Consensus CDS
    CCDS56242.1
    UniProtKB/Swiss-Prot
    Q01826
    Related
    ENSP00000399518.1, ENST00000417717.6
    Conserved Domains (4) summary
    smart00389
    Location:676 → 733
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  3. NM_001322871.2 → NP_001309800.1  DNA-binding protein SATB1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS56242.1
    UniProtKB/Swiss-Prot
    Q01826
    Conserved Domains (4) summary
    smart00389
    Location:676 → 733
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  4. NM_001322872.2 → NP_001309801.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    B3KXF1, C9JTR6, Q01826, Q59EQ0
    Related
    ENSP00000514848.1, ENST00000700180.1
    Conserved Domains (4) summary
    smart00389
    Location:644 → 701
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  5. NM_001322873.2 → NP_001309802.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    B3KXF1, C9JTR6, Q01826, Q59EQ0
    Conserved Domains (4) summary
    smart00389
    Location:644 → 701
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  6. NM_001322874.2 → NP_001309803.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    B3KXF1, C9JTR6, Q01826, Q59EQ0
    Related
    ENSP00000390529.2, ENST00000415069.6
    Conserved Domains (4) summary
    smart00389
    Location:644 → 701
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  7. NM_001322875.2 → NP_001309804.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    B3KXF1, C9JTR6, Q01826, Q59EQ0
    Related
    ENSP00000514846.1, ENST00000700178.1
    Conserved Domains (4) summary
    smart00389
    Location:644 → 701
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  8. NM_001322876.2 → NP_001309805.1  DNA-binding protein SATB1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521

  9. NM_002971.6 → NP_002962.1  DNA-binding protein SATB1 isoform 1

    See identical proteins and their annotated locations for NP_002962.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, compared to variant 3. Isoform 1 has a shorter C-terminus, compared to isoform 2.
    Source sequence(s)
    AA001621, AB209761, AC139618, AC144521, AK127242, BC001744, DA938384
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    B3KXF1, C9JTR6, Q01826, Q59EQ0
    Related
    ENSP00000341024.5, ENST00000338745.11
    Conserved Domains (4) summary
    smart00389
    Location:644 → 701
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    18345377..18445592 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533989.3 → XP_011532291.1  DNA-binding protein SATB1 isoform X1

    See identical proteins and their annotated locations for XP_011532291.1

    UniProtKB/Swiss-Prot
    Q01826
    Conserved Domains (4) summary
    smart00389
    Location:676 → 733
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  2. XM_011533988.4 → XP_011532290.1  DNA-binding protein SATB1 isoform X1

    See identical proteins and their annotated locations for XP_011532290.1

    UniProtKB/Swiss-Prot
    Q01826
    Conserved Domains (4) summary
    smart00389
    Location:676 → 733
    HOX; Homeodomain
    pfam02376
    Location:497 → 567
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:176 → 246
    CUTL; CUT1-like DNA-binding domain of SATB

  3. XM_047448683.1 → XP_047304639.1  DNA-binding protein SATB1 isoform X2

  4. XM_011533990.4 → XP_011532292.1  DNA-binding protein SATB1 isoform X2

    Conserved Domains (3) summary
    pfam02376
    Location:372 → 443
    CUT; CUT domain
    pfam16534
    Location:72 → 170
    ULD; Ubiquitin-like oligomerization domain of SATB
    pfam16557
    Location:200 → 247
    CUTL; CUT1-like DNA-binding domain of SATB

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    18347503..18447703 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347482.1 → XP_054203457.1  DNA-binding protein SATB1 isoform X1

  2. XM_054347481.1 → XP_054203456.1  DNA-binding protein SATB1 isoform X1

  3. XM_054347484.1 → XP_054203459.1  DNA-binding protein SATB1 isoform X2

  4. XM_054347483.1 → XP_054203458.1  DNA-binding protein SATB1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q01826.1 GenPept UniProtKB/Swiss-Prot:Q01826

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