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    SATB2 SATB homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 23314, updated on 3-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    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
    Chromosome 2q32-q33 deletion syndrome
    MedGen: C2676739 OMIM: 612313 GeneReviews: SATB2-Associated Syndrome
    Compare labs

    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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ21474, FLJ32076, KIAA1034, MGC119474, MGC119477

    Gene Ontology Provided by GOA

    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

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

    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_016976.2 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001172509.2NP_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:614671
      HOX; Homeodomain
      cd11585
      Location:60155
      SATB1_N; N-terminal domain of SATB1 and similar proteins
      pfam02376
      Location:477556
      CUT; CUT domain
      pfam16557
      Location:162232
      CUTL; CUT1-like DNA-binding domain of SATB
    2. NM_001172517.1NP_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:614671
      HOX; Homeodomain
      cd11585
      Location:60155
      SATB1_N; N-terminal domain of SATB1 and similar proteins
      pfam02376
      Location:477556
      CUT; CUT domain
      pfam16557
      Location:162232
      CUTL; CUT1-like DNA-binding domain of SATB
    3. NM_015265.4NP_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:614671
      HOX; Homeodomain
      cd11585
      Location:60155
      SATB1_N; N-terminal domain of SATB1 and similar proteins
      pfam02376
      Location:477556
      CUT; CUT domain
      pfam16557
      Location:162232
      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_005246396.4XP_005246453.1  DNA-binding protein SATB2 isoform X2

      UniProtKB/TrEMBL
      B3KPQ9
      Conserved Domains (4) summary
      smart00389
      Location:556613
      HOX; Homeodomain
      cd11585
      Location:297
      SATB1_N; N-terminal domain of SATB1 and similar proteins
      pfam02376
      Location:419497
      CUT; CUT domain
      pfam16557
      Location:128175
      CUTL; CUT1-like DNA-binding domain of SATB
    2. XM_047443775.1XP_047299731.1  DNA-binding protein SATB2 isoform X1

      UniProtKB/Swiss-Prot
      A8K5Z8, Q3ZB87, Q4V763, Q9UPW6
      UniProtKB/TrEMBL
      B3KPQ9
      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_054341120.1XP_054197095.1  DNA-binding protein SATB2 isoform X1

      UniProtKB/Swiss-Prot
      A8K5Z8, Q3ZB87, Q4V763, Q9UPW6
      UniProtKB/TrEMBL
      B3KPQ9
    2. XM_054341121.1XP_054197096.1  DNA-binding protein SATB2 isoform X2

      UniProtKB/TrEMBL
      B3KPQ9
    3. XM_054341122.1XP_054197097.1  DNA-binding protein SATB2 isoform X3

      UniProtKB/TrEMBL
      C9JR56
    4. XM_054341123.1XP_054197098.1  DNA-binding protein SATB2 isoform X3

      UniProtKB/TrEMBL
      C9JR56