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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
    mouse all
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    Genomic context

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    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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    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

    Gene LinkOut

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