SATB2 SATB homeobox 2 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathogenic SATB2 missense variants affecting p.Gly392 have variable functional implications and result in diverse clinical phenotypes.
Title: Pathogenic SATB2 missense variants affecting p.Gly392 have variable functional implications and result in diverse clinical phenotypes.
SATB2 Cytoplasmic Expression is Characteristic of a Subset of Ovarian Stromal Cells and Sex Cord Stromal Tumors.
Title: SATB2 Cytoplasmic Expression is Characteristic of a Subset of Ovarian Stromal Cells and Sex Cord Stromal Tumors.
Concomitant expression patterns of CDX2 and SATB2 as prognostic factors in stage III colorectal cancers.
Title: Concomitant expression patterns of CDX2 and SATB2 as prognostic factors in stage III colorectal cancers.
SATB2 organizes the 3D genome architecture of cognition in cortical neurons.
Title: SATB2 organizes the 3D genome architecture of cognition in cortical neurons.
Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1.
Title: Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1.
Progress of epigenetic modification of SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate.
Title: Progress of epigenetic modification of SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate.
Single-cell sequencing reveals SATB2/NOTCH1 signaling promotes the progression of malignancy of epithelial cells from papillary thyroid cancer.
Title: Single-cell sequencing reveals SATB2/NOTCH1 signaling promotes the progression of malignancy of epithelial cells from papillary thyroid cancer.
Evaluation of Lineage/Site-specific Nuclear Immunohistochemical Markers SATB2, Cyclin D1, SALL4, and BCOR in High-grade Endometrial Carcinomas.
Title: Evaluation of Lineage/Site-specific Nuclear Immunohistochemical Markers SATB2, Cyclin D1, SALL4, and BCOR in High-grade Endometrial Carcinomas.
microRNA-660 Enhances Cisplatin Sensitivity via Decreasing SATB2 Expression in Lung Adenocarcinoma.
Title: microRNA-660 Enhances Cisplatin Sensitivity via Decreasing SATB2 Expression in Lung Adenocarcinoma.
YAP-Activated SATB2 Is a Coactivator of NRF2 That Amplifies Antioxidative Capacity and Promotes Tumor Progression in Renal Cell Carcinoma.
Title: YAP-Activated SATB2 Is a Coactivator of NRF2 That Amplifies Antioxidative Capacity and Promotes Tumor Progression in Renal Cell Carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (135)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Satb2 (e-PCR), detects polymorphism
- UniSTS:498445

D2S2708 (e-PCR)
- UniSTS:21036

RH121822 (e-PCR)
- UniSTS:134971

D2S1498E (e-PCR)
- UniSTS:150341

RH80503 (e-PCR)
- UniSTS:87202

WI-17677 (e-PCR)
- UniSTS:45735

SHGC-83346 (e-PCR)
- UniSTS:101047

RH91707 (e-PCR)
- UniSTS:91093

A006V05 (e-PCR)
- UniSTS:65279

Clone Names

FLJ21474, FLJ32076, KIAA1034, MGC119474, MGC119477

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables histone deacetylase binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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

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Preferred Names: DNA-binding protein SATB2

Names: SATB family member 2; SATB2 fusion; special AT-rich sequence-binding protein 2

NCBI Reference Sequences (RefSeq)

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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

NG_016976.2 RefSeqGene

Range

18328..206762

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001172509.2 → NP_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:614 → 671

HOX; Homeodomain

cd11585
Location:60 → 155

SATB1_N; N-terminal domain of SATB1 and similar proteins

pfam02376
Location:477 → 556

CUT; CUT domain

pfam16557
Location:162 → 232

CUTL; CUT1-like DNA-binding domain of SATB
NM_001172517.1 → NP_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:614 → 671

HOX; Homeodomain

cd11585
Location:60 → 155

SATB1_N; N-terminal domain of SATB1 and similar proteins

pfam02376
Location:477 → 556

CUT; CUT domain

pfam16557
Location:162 → 232

CUTL; CUT1-like DNA-binding domain of SATB
NM_015265.4 → NP_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:614 → 671

HOX; Homeodomain

cd11585
Location:60 → 155

SATB1_N; N-terminal domain of SATB1 and similar proteins

pfam02376
Location:477 → 556

CUT; CUT domain

pfam16557
Location:162 → 232

CUTL; CUT1-like DNA-binding domain of SATB

RNA

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

199269500..199471266 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005246396.4 → XP_005246453.1 DNA-binding protein SATB2 isoform X2

UniProtKB/TrEMBL

B3KPQ9

Conserved Domains (4) summary

smart00389
Location:556 → 613

HOX; Homeodomain

cd11585
Location:2 → 97

SATB1_N; N-terminal domain of SATB1 and similar proteins

pfam02376
Location:419 → 497

CUT; CUT domain

pfam16557
Location:128 → 175

CUTL; CUT1-like DNA-binding domain of SATB
XM_047443775.1 → XP_047299731.1 DNA-binding protein SATB2 isoform X1

UniProtKB/Swiss-Prot

A8K5Z8, Q3ZB87, Q4V763, Q9UPW6

Related

ENSP00000514854.1, ENST00000700193.1