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SATB2 SATB homeobox 2 [ Homo sapiens (human) ]

Gene ID: 23314, updated on 15-Jun-2019

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
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
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

Genomic context

See SATB2 in Genome Data Viewer
Location:
2q33.1
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (199269500..199471266, complement)
105 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 RNA, U7 small nuclear 147 pseudogene 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 FunctionsWhat'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 (2012-02-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-02-23)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study of sleep habits and insomnia.
NHGRI GWA Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
NHGRI GWA Catalog
Genome-wide association of body fat distribution in African ancestry populations suggests new loci.
NHGRI GWA Catalog
Integrative genome-wide association analysis of cytoarchitectural abnormalities in the prefrontal cortex of psychiatric disorders.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21474, FLJ32076, KIAA1034, MGC119474, MGC119477

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cartilage development IEA
Inferred from Electronic Annotation
more info
 
cellular response to organic substance IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
commitment of neuronal cell to specific neuron type in forebrain IEA
Inferred from Electronic Annotation
more info
 
embryonic pattern specification IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
neuron migration IEA
Inferred from Electronic Annotation
more info
 
osteoblast development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
histone deacetylase complex IEA
Inferred from Electronic Annotation
more info
 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5001..206767
    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
    Q9UPW6
    UniProtKB/TrEMBL
    A0A024R3U6, 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:477555
    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
    Q9UPW6
    UniProtKB/TrEMBL
    A0A024R3U6, Q59FT3
    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:477555
    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
    Q9UPW6
    UniProtKB/TrEMBL
    A0A024R3U6
    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:477555
    CUT; CUT domain
    pfam16557
    Location:162232
    CUTL; CUT1-like DNA-binding domain of SATB

RNA

  1. NR_134967.1 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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    199269500..199471266 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003656.1XP_016859145.1  DNA-binding protein SATB2 isoform X2

    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_005246396.3XP_005246453.1  DNA-binding protein SATB2 isoform X2

    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
  3. XM_024452767.1XP_024308535.1  DNA-binding protein SATB2 isoform X3

    Conserved Domains (3) summary
    smart00389
    Location:473530
    HOX; Homeodomain
    pfam02376
    Location:336414
    CUT; CUT domain
    pfam16557
    Location:2191
    CUTL; CUT1-like DNA-binding domain of SATB
  4. XM_024452768.1XP_024308536.1  DNA-binding protein SATB2 isoform X3

    Conserved Domains (3) summary
    smart00389
    Location:473530
    HOX; Homeodomain
    pfam02376
    Location:336414
    CUT; CUT domain
    pfam16557
    Location:2191
    CUTL; CUT1-like DNA-binding domain of SATB
  5. XM_011510840.3XP_011509142.1  DNA-binding protein SATB2 isoform X1

    See identical proteins and their annotated locations for XP_011509142.1

    UniProtKB/Swiss-Prot
    Q9UPW6
    UniProtKB/TrEMBL
    A0A024R3U6
    Related
    ENSP00000388581.1, ENST00000428695.5
    Conserved Domains (4) summary
    smart00389
    Location:614671
    HOX; Homeodomain
    cd11585
    Location:60155
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:477555
    CUT; CUT domain
    pfam16557
    Location:162232
    CUTL; CUT1-like DNA-binding domain of SATB
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