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SATB1 SATB homeobox 1 [ Homo sapiens (human) ]

Gene ID: 6304, updated on 7-Dec-2018

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
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
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

Genomic context

See SATB1 in Genome Data Viewer
Location:
3p24.3
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (18345388..18445588, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (18389133..18480265, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phosducin-like 3 pseudogene 3 Neighboring gene uncharacterized LOC339862 Neighboring gene VISTA enhancer hs250 Neighboring gene SATB1 antisense RNA 1 Neighboring gene RAD23B pseudogene 1 Neighboring gene uncharacterized LOC105376976

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

NHGRI GWAS Catalog

Description
New gene functions in megakaryopoiesis and platelet formation.
NHGRI GWA Catalog
Susceptibility to chronic mucus hypersecretion, a genome wide association study.
NHGRI GWA Catalog

Pathways from BioSystems

  • Apoptosis, organism-specific biosystem (from REACTOME)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptotic cleavage of cellular proteins, organism-specific biosystem (from REACTOME)
    Apoptotic cleavage of cellular proteins, organism-specific biosystemApoptotic cell death is achieved by the caspase-mediatedcleavage of various vital proteins. Among caspase targets are proteins such as E-cadherin, Beta-catenin, alpha fodrin, GAS2, FADK, alpha adduc...
  • Apoptotic execution phase, organism-specific biosystem (from REACTOME)
    Apoptotic execution phase, organism-specific biosystemIn the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucle...
  • Caspase cascade in apoptosis, organism-specific biosystem (from Pathway Interaction Database)
    Caspase cascade in apoptosis, organism-specific biosystem
    Caspase cascade in apoptosis
  • Programmed Cell Death, organism-specific biosystem (from REACTOME)
    Programmed Cell Death, organism-specific biosystemCell death is a fundamental cellular response that has a crucial role in shaping our bodies during development and in regulating tissue homeostasis by eliminating unwanted cells. There are a number o...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
CD4-positive, alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
CD8-positive, alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
activated T cell proliferation IEA
Inferred from Electronic Annotation
more info
 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
epidermis development IEA
Inferred from Electronic Annotation
more info
 
histone methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
reflex IEA
Inferred from Electronic Annotation
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
PML body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear heterochromatin 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 
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)

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
    11816..105201
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001131010.3NP_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
    Q01826
    UniProtKB/TrEMBL
    A0A024R2H1
    Related
    ENSP00000399708.2, ENST00000454909.6
    Conserved Domains (4) summary
    smart00389
    Location:644701
    HOX; Homeodomain
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  2. NM_001195470.2NP_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
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  3. NM_001322871.1NP_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
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  4. NM_001322872.1NP_001309801.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    Q01826
    UniProtKB/TrEMBL
    A0A024R2H1
    Conserved Domains (4) summary
    smart00389
    Location:644701
    HOX; Homeodomain
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  5. NM_001322873.1NP_001309802.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    Q01826
    UniProtKB/TrEMBL
    A0A024R2H1
    Conserved Domains (4) summary
    smart00389
    Location:644701
    HOX; Homeodomain
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  6. NM_001322874.1NP_001309803.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    Q01826
    UniProtKB/TrEMBL
    A0A024R2H1
    Conserved Domains (4) summary
    smart00389
    Location:644701
    HOX; Homeodomain
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  7. NM_001322875.1NP_001309804.1  DNA-binding protein SATB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC139618, AC144521
    Consensus CDS
    CCDS2631.1
    UniProtKB/Swiss-Prot
    Q01826
    UniProtKB/TrEMBL
    A0A024R2H1
    Conserved Domains (4) summary
    smart00389
    Location:644701
    HOX; Homeodomain
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  8. NM_001322876.1NP_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
    Q01826
    UniProtKB/TrEMBL
    A0A024R2H1
    Related
    ENSP00000341024.5, ENST00000338745.10
    Conserved Domains (4) summary
    smart00389
    Location:644701
    HOX; Homeodomain
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB

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.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    18345388..18445588 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533989.2XP_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
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  2. XM_011533988.3XP_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
    cd11585
    Location:74169
    SATB1_N; N-terminal domain of SATB1 and similar proteins
    pfam02376
    Location:366443
    CUT; CUT domain
    pfam16557
    Location:176246
    CUTL; CUT1-like DNA-binding domain of SATB
  3. XM_011533990.3XP_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
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