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GATA3 GATA binding protein 3 [ Homo sapiens (human) ]

Gene ID: 2625, updated on 22-Jan-2023

Summary

Official Symbol
GATA3provided by HGNC
Official Full Name
GATA binding protein 3provided by HGNC
Primary source
HGNC:HGNC:4172
See related
Ensembl:ENSG00000107485 MIM:131320; AllianceGenome:HGNC:4172
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
HDR; HDRS
Summary
This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is an important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia. [provided by RefSeq, Nov 2009]
Expression
Biased expression in skin (RPKM 54.6), urinary bladder (RPKM 20.0) and 7 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See GATA3 in Genome Data Viewer
Location:
10p14
Exon count:
9
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (8045333..8075198)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (8055568..8076094)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (8096651..8117161)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene TATA-box binding protein associated factor 3 Neighboring gene Sharpr-MPRA regulatory region 13617 Neighboring gene uncharacterized LOC105376394 Neighboring gene GATA3 antisense RNA 1 Neighboring gene uncharacterized LOC105376395 Neighboring gene PRP38 domain containing A pseudogene 1

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
Hypoparathyroidism, deafness, renal disease syndrome
MedGen: C1840333 OMIM: 146255 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-06-24)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-06-24)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
EBI GWAS Catalog
A genome-wide association study of Hodgkin's lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3).
EBI GWAS Catalog
A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.
EBI GWAS Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog
Genome-wide diet-gene interaction analyses for risk of colorectal cancer.
EBI GWAS Catalog
Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations.
EBI GWAS Catalog
Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype.
EBI GWAS Catalog
Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin's lymphoma.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Amino acids 19-26 of HIV-1 Nef mediate the binding of Nef to murine GATA-1 and GATA-3 in vitro, suggesting Nef may act as a nuclear regulatory factor through binding to human GATA-1 and GATA-3 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

Homology

Clone Names

  • MGC2346, MGC5199, MGC5445

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables E-box binding IDA
Inferred from Direct Assay
more info
PubMed 
enables HMG box domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
 
enables interleukin-2 receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription coactivator binding IEA
Inferred from Electronic Annotation
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within T cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in T cell receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in T-helper 2 cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in TOR signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in anatomical structure formation involved in morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
involved_in aortic valve morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in axon guidance IEA
Inferred from Electronic Annotation
more info
 
involved_in canonical Wnt signaling pathway involved in metanephric kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cardiac right ventricle morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell fate determination ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cell maturation IEA
Inferred from Electronic Annotation
more info
 
involved_in cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to BMP stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to interferon-alpha IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to interleukin-4 IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to tumor necrosis factor IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
involved_in cochlea development IEA
Inferred from Electronic Annotation
more info
 
involved_in defense response TAS
Traceable Author Statement
more info
PubMed 
involved_in developmental growth IEA
Inferred from Electronic Annotation
more info
 
involved_in ear development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic hemopoiesis IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic organ development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in humoral immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in immune system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
involved_in inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in inner ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lens development in camera-type eye IEA
Inferred from Electronic Annotation
more info
 
involved_in lymphocyte migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in macrophage differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in male gonad development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in mast cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in mesenchymal to epithelial transition IDA
Inferred from Direct Assay
more info
PubMed 
involved_in mesonephros development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in natural killer cell activation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of DNA demethylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell motility IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of cell proliferation involved in mesonephros development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of endothelial cell apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of negative regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of inflammatory response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of interleukin-2 production IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of mammary gland epithelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of type II interferon production IEA
Inferred from Electronic Annotation
more info
 
involved_in nephric duct formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nephric duct morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
 
involved_in norepinephrine biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in otic vesicle development IEA
Inferred from Electronic Annotation
more info
 
involved_in parathyroid gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in parathyroid hormone secretion IEA
Inferred from Electronic Annotation
more info
 
involved_in pharyngeal system development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in phosphatidylinositol 3-kinase signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of T-helper 2 cell cytokine production IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of endothelial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of histone H3-K14 acetylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of histone H3-K9 acetylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of interleukin-13 production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of interleukin-13 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of interleukin-4 production ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of interleukin-5 production IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of miRNA transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of protein kinase B signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of thyroid hormone generation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription regulatory region DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of ureteric bud formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
involved_in pro-T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of T-helper cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of cellular response to X-ray IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of epithelial cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of establishment of cell polarity IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of histone H3-K27 methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of histone H3-K4 methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of nephron tubule epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of neuron projection development IEA
Inferred from Electronic Annotation
more info
 
involved_in response to estrogen IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ethanol IEA
Inferred from Electronic Annotation
more info
 
involved_in response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
involved_in response to virus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in sympathetic nervous system development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in thymic T cell selection IEA
Inferred from Electronic Annotation
more info
 
involved_in thymus development IEA
Inferred from Electronic Annotation
more info
 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in type IV hypersensitivity IEA
Inferred from Electronic Annotation
more info
 
involved_in ureter maturation IEA
Inferred from Electronic Annotation
more info
 
involved_in ureter morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in ureteric bud formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in uterus development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in ventricular septum development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
trans-acting T-cell-specific transcription factor GATA-3
Names
GATA-binding factor 3

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_015859.2 RefSeqGene

    Range
    14357..34867
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001002295.2NP_001002295.1  trans-acting T-cell-specific transcription factor GATA-3 isoform 1

    See identical proteins and their annotated locations for NP_001002295.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AI024501, AI686327, AL390294, BC003070, BC006793, BC006839, BM152193
    Consensus CDS
    CCDS31143.1
    UniProtKB/Swiss-Prot
    P23771
    Related
    ENSP00000368632.3, ENST00000379328.9
    Conserved Domains (2) summary
    smart00401
    Location:313362
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:317367
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  2. NM_002051.3NP_002042.1  trans-acting T-cell-specific transcription factor GATA-3 isoform 2

    See identical proteins and their annotated locations for NP_002042.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the mid-coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1.
    Source sequence(s)
    AI024501, AI686327, AL390294, BC006793, BC006839, BM152193
    Consensus CDS
    CCDS7083.1
    UniProtKB/Swiss-Prot
    P23771, Q96J16
    Related
    ENSP00000341619.3, ENST00000346208.4
    Conserved Domains (2) summary
    smart00401
    Location:312361
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:316366
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    8045333..8075198
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005252443.6XP_005252500.1  trans-acting T-cell-specific transcription factor GATA-3 isoform X1

    See identical proteins and their annotated locations for XP_005252500.1

    UniProtKB/Swiss-Prot
    P23771
    Conserved Domains (2) summary
    smart00401
    Location:313362
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:317367
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  2. XM_047425045.1XP_047281001.1  trans-acting T-cell-specific transcription factor GATA-3 isoform X2

    UniProtKB/Swiss-Prot
    Q96J16
  3. XM_005252442.3XP_005252499.1  trans-acting T-cell-specific transcription factor GATA-3 isoform X1

    See identical proteins and their annotated locations for XP_005252499.1

    UniProtKB/Swiss-Prot
    P23771
    Conserved Domains (2) summary
    smart00401
    Location:313362
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:317367
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  4. XM_047425044.1XP_047281000.1  trans-acting T-cell-specific transcription factor GATA-3 isoform X2

    UniProtKB/Swiss-Prot
    Q96J16

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    8055568..8076094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)