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    SATB1 SATB homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 6304, updated on 27-Nov-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SATB1 in Genome Data Viewer
    Location:
    3p24.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (18345377..18445592, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (18347503..18447703, complement)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Developmental delay with dysmorphic facies and dental anomalies
    MedGen: C5543197 OMIM: 619228 GeneReviews: Not available
    not available
    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in 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

    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)

    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_001131010.4NP_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:644701
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    2. NM_001195470.3NP_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:676733
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    3. NM_001322871.2NP_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:676733
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    4. NM_001322872.2NP_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:644701
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    5. NM_001322873.2NP_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:644701
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    6. NM_001322874.2NP_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:644701
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    7. NM_001322875.2NP_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:644701
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    8. NM_001322876.2NP_001309805.1  DNA-binding protein SATB1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC139618, AC144521
    9. NM_002971.6NP_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:644701
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB

    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_000003.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_011533989.3XP_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:676733
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    2. XM_011533988.4XP_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:676733
      HOX; Homeodomain
      pfam02376
      Location:497567
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:176246
      CUTL; CUT1-like DNA-binding domain of SATB
    3. XM_047448683.1XP_047304639.1  DNA-binding protein SATB1 isoform X2

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

      Conserved Domains (3) summary
      pfam02376
      Location:372443
      CUT; CUT domain
      pfam16534
      Location:72170
      ULD; Ubiquitin-like oligomerization domain of SATB
      pfam16557
      Location:200247
      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_054347482.1XP_054203457.1  DNA-binding protein SATB1 isoform X1

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

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

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