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SATB2 SATB homeobox 2 [ Homo sapiens (human) ]

Gene ID: 23314, updated on 4-Jan-2025

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
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

General gene information

Clone Names

  • FLJ21474, FLJ32076, KIAA1034, MGC119474, MGC119477

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cartilage development  
involved_in chromatin remodeling  
involved_in embryonic pattern specification  
involved_in embryonic skeletal system morphogenesis  
involved_in negative regulation of transcription by RNA polymerase II  
involved_in neuron migration  
involved_in osteoblast development  
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in regulation of transcription by RNA polymerase II  
involved_in roof of mouth development  
Component Evidence Code Pubs
located_in chromatin  
part_of histone deacetylase complex  
located_in nuclear matrix  
located_in nucleoplasm  
located_in nucleoplasm  
part_of transcription regulator complex  

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
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