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    Satb1 special AT-rich sequence binding protein 1 [ Mus musculus (house mouse) ]

    Gene ID: 20230, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Satb1provided by MGI
    Official Full Name
    special AT-rich sequence binding protein 1provided by MGI
    Primary source
    MGI:MGI:105084
    See related
    Ensembl:ENSMUSG00000023927 AllianceGenome:MGI:105084
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    2610306G12Rik
    Summary
    Enables several functions, including DNA-binding transcription factor activity; DNA-binding transcription factor binding activity; and chromatin binding activity. Acts upstream of or within several processes, including T cell activation; negative regulation of transcription by RNA polymerase II; and reflex. Located in heterochromatin and nuclear matrix. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Used to study Sjogren's syndrome. Orthologous to human SATB1 (SATB homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in thymus adult (RPKM 74.6), cortex adult (RPKM 7.3) and 5 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Satb1 in Genome Data Viewer
    Location:
    17 C; 17 26.81 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (52043215..52140318, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (51736187..51833290, complement)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene 60S ribosomal protein L26 pseudogene Neighboring gene predicted gene, 31143 Neighboring gene STARR-seq mESC enhancer starr_42807 Neighboring gene STARR-seq mESC enhancer starr_42808 Neighboring gene STARR-seq mESC enhancer starr_42810 Neighboring gene STARR-positive B cell enhancer ABC_E10962 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:51972530-51972717 Neighboring gene STARR-seq mESC enhancer starr_42811 Neighboring gene STARR-seq mESC enhancer starr_42812 Neighboring gene predicted gene 6934 Neighboring gene predicted gene, 54011 Neighboring gene STARR-positive B cell enhancer mm9_chr17:52043120-52043421 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:52043404-52043557 Neighboring gene predicted gene, 20098 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:52095713-52095914

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. SATB1 prevents immune cell infiltration by regulating chromatin organization and gene expression of a chemokine gene cluster in T cells. Wang B, et al. Commun Biol, 2024 Oct 11. PMID 39394451, Free PMC Article
    2. Regulation of SATB1 during thymocyte development by TCR signaling. Gottimukkala KP, et al. Mol Immunol, 2016 Sep. PMID 27454343, Free PMC Article
    3. Nicotinamide induces apoptosis of F9 mouse teratocarcinoma stem cells by downregulation of SATB1 expression. Zhang Y, et al. Tumour Biol, 2015 Jun. PMID 25596087
    4. Crystal structure of the ubiquitin-like domain-CUT repeat-like tandem of special AT-rich sequence binding protein 1 (SATB1) reveals a coordinating DNA-binding mechanism. Wang Z, et al. J Biol Chem, 2014 Oct 3. PMID 25124042, Free PMC Article
    5. Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases. Sommer D, et al. Nat Commun, 2014. PMID 24413636

    See all (117) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SATB1 prevents immune cell infiltration by regulating chromatin organization and gene expression of a chemokine gene cluster in T cells.
      Title: SATB1 prevents immune cell infiltration by regulating chromatin organization and gene expression of a chemokine gene cluster in T cells.
    2. Long Non-Coding RNA ANRIL Regulates Inflammatory Factor Expression in Ulcerative Colitis Via the miR-191-5p/SATB1 Axis.
      Title: Long Non-Coding RNA ANRIL Regulates Inflammatory Factor Expression in Ulcerative Colitis Via the miR-191-5p/SATB1 Axis.
    3. A dual function for the chromatin organizer Special A-T rich Binding Protein 1 in B-lineage cells.
      Title: A dual function for the chromatin organizer Special A-T rich Binding Protein 1 in B-lineage cells.
    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. Crucial Roles of SATB1 in Regulation of Thymocyte Migration after Positive Selection.
      Title: Crucial Roles of SATB1 in Regulation of Thymocyte Migration after Positive Selection.
    6. Identification of a novel enhancer essential for Satb1 expression in TH2 cells and activated ILC2s.
      Title: Identification of a novel enhancer essential for Satb1 expression in T(H)2 cells and activated ILC2s.
    7. The role of selective SATB1 deletion in somatostatin expressing interneurons on endogenous network activity and the transition to epilepsy.
      Title: The role of selective SATB1 deletion in somatostatin expressing interneurons on endogenous network activity and the transition to epilepsy.
    8. Reduced Satb1 expression predisposes CD4(+) T conventional cells to Treg suppression and promotes transplant survival.
      Title: Reduced Satb1 expression predisposes CD4(+) T conventional cells to Treg suppression and promotes transplant survival.
    9. SATB1 ensures appropriate transcriptional programs within naive CD8(+) T cells.
      Title: SATB1 ensures appropriate transcriptional programs within naïve CD8(+) T cells.
    10. Special AT-Rich Sequence-Binding Protein 1 Supports Survival and Maturation of Naive B Cells Stimulated by B Cell Receptors.
      Title: Special AT-Rich Sequence-Binding Protein 1 Supports Survival and Maturation of Naive B Cells Stimulated by B Cell Receptors.
    Submit: New GeneRIF Correction See all GeneRIFs (53)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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 MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity 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 binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within CD4-positive, alpha-beta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within CD8-positive, alpha-beta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within T cell activation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within activated T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within chromatin organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within epidermis development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within reflex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DNA-binding protein SATB1

    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.

    mRNA and Protein(s)

    1. NM_001163630.1 → NP_001157102.1  DNA-binding protein SATB1 isoform 1

      See identical proteins and their annotated locations for NP_001157102.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC131975, AK037740, AK081385, AK158518, AW045567, CV556064
      Consensus CDS
      CCDS28876.1
      UniProtKB/Swiss-Prot
      Q60611, Q91XB1
      Related
      ENSMUSP00000119842.3, ENSMUST00000152830.9
      Conserved Domains (4) summary
      smart00389
      Location:645 → 702
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    2. NM_001163631.1 → NP_001157103.1  DNA-binding protein SATB1 isoform 1

      See identical proteins and their annotated locations for NP_001157103.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC131975, AK037740, AK081385, AK134040, AW045567, BB611616
      Consensus CDS
      CCDS28876.1
      UniProtKB/Swiss-Prot
      Q60611, Q91XB1
      Related
      ENSMUSP00000128841.2, ENSMUST00000169480.8
      Conserved Domains (4) summary
      smart00389
      Location:645 → 702
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    3. NM_001163632.1 → NP_001157104.1  DNA-binding protein SATB1 isoform 1

      See identical proteins and their annotated locations for NP_001157104.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC131975, AC154796, AK037740, AK081385, AK134040, AW045567
      Consensus CDS
      CCDS28876.1
      UniProtKB/Swiss-Prot
      Q60611, Q91XB1
      Related
      ENSMUSP00000120536.2, ENSMUST00000133574.8
      Conserved Domains (4) summary
      smart00389
      Location:645 → 702
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    4. NM_001357636.1 → NP_001344565.1  DNA-binding protein SATB1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC131975, AC154796, AW045567
      Conserved Domains (4) summary
      smart00389
      Location:677 → 734
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    5. NM_001357637.1 → NP_001344566.1  DNA-binding protein SATB1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC131975, AC154796, AW045567
      Conserved Domains (4) summary
      smart00389
      Location:644 → 701
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    6. NM_001357638.1 → NP_001344567.1  DNA-binding protein SATB1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC131975, AC154796, AW045567
      Consensus CDS
      CCDS28876.1
      UniProtKB/Swiss-Prot
      Q60611, Q91XB1
      Conserved Domains (4) summary
      smart00389
      Location:645 → 702
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    7. NM_001357640.1 → NP_001344569.1  DNA-binding protein SATB1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC131975, AC154796, AW045567
      Conserved Domains (4) summary
      smart00389
      Location:625 → 682
      HOX; Homeodomain
      cd11585
      Location:74 → 169
      SATB1_N; N-terminal domain of SATB1 and similar proteins
      pfam02376
      Location:366 → 443
      CUT; CUT domain
      pfam16557
      Location:176 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    8. NM_009122.2 → NP_033148.2  DNA-binding protein SATB1 isoform 1

      See identical proteins and their annotated locations for NP_033148.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same protein.
      Source sequence(s)
      AC131975, AK037740, AK081385, AK134040, AW045567
      Consensus CDS
      CCDS28876.1
      UniProtKB/Swiss-Prot
      Q60611, Q91XB1
      Related
      ENSMUSP00000116006.2, ENSMUST00000144331.8
      Conserved Domains (4) summary
      smart00389
      Location:645 → 702
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      52043215..52140318 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006523926.5 → XP_006523989.1  DNA-binding protein SATB1 isoform X1

      See identical proteins and their annotated locations for XP_006523989.1

      Conserved Domains (4) summary
      smart00389
      Location:677 → 734
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    2. XM_006523925.3 → XP_006523988.1  DNA-binding protein SATB1 isoform X1

      See identical proteins and their annotated locations for XP_006523988.1

      Conserved Domains (4) summary
      smart00389
      Location:677 → 734
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    3. XM_017317366.3 → XP_017172855.1  DNA-binding protein SATB1 isoform X3

      Conserved Domains (4) summary
      smart00389
      Location:593 → 650
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    4. XM_006523924.4 → XP_006523987.1  DNA-binding protein SATB1 isoform X1

      See identical proteins and their annotated locations for XP_006523987.1

      Conserved Domains (4) summary
      smart00389
      Location:677 → 734
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB

    5. XM_036160424.1 → XP_036016317.1  DNA-binding protein SATB1 isoform X4

      Conserved Domains (4) summary
      smart00389
      Location:592 → 649
      HOX; Homeodomain
      pfam02376
      Location:372 → 444
      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. XM_006523927.5 → XP_006523990.1  DNA-binding protein SATB1 isoform X2

      UniProtKB/TrEMBL
      E9PVB7
      Related
      ENSMUSP00000118839.2, ENSMUST00000140979.8
      Conserved Domains (4) summary
      smart00389
      Location:676 → 733
      HOX; Homeodomain
      pfam02376
      Location:372 → 439
      CUT; CUT domain
      pfam16534
      Location:72 → 170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:180 → 246
      CUTL; CUT1-like DNA-binding domain of SATB
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q60611.2 GenPept UniProtKB/Swiss-Prot:Q60611

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