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Aliases for GATAD2B Gene

Aliases for GATAD2B Gene

  • GATA Zinc Finger Domain Containing 2B 2 3 5
  • Transcription Repressor P66 Beta Component Of The MeCP1 Complex 2 3
  • GATA Zinc Finger Domain-Containing Protein 2B 3 4
  • Transcriptional Repressor P66-Beta 3
  • KIAA1150 4
  • P66beta 3
  • P66/P68 4
  • MRD18 3
  • P68 3

External Ids for GATAD2B Gene

Previous GeneCards Identifiers for GATAD2B Gene

  • GC01M150593
  • GC01M152044
  • GC01M153777
  • GC01M125139

Summaries for GATAD2B Gene

Entrez Gene Summary for GATAD2B Gene

  • This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]

GeneCards Summary for GATAD2B Gene

GATAD2B (GATA Zinc Finger Domain Containing 2B) is a Protein Coding gene. Diseases associated with GATAD2B include Mental Retardation, Autosomal Dominant 18 and Koolen-De Vries Syndrome. Among its related pathways are Gene Expression and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is GATAD2A.

UniProtKB/Swiss-Prot for GATAD2B Gene

  • Transcriptional repressor. Enhances MBD2-mediated repression. Efficient repression requires the presence of GATAD2A. Targets MBD3 to discrete loci in the nucleus. May play a role in synapse development.

Gene Wiki entry for GATAD2B Gene

Additional gene information for GATAD2B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GATAD2B Gene

Genomics for GATAD2B Gene

GeneHancer (GH) Regulatory Elements for GATAD2B Gene

Promoters and enhancers for GATAD2B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J153919 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +1.6 1568 5.4 PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B GATAD2B LOC101928059 UBAP2L CRTC2 ILF2 INTS3 CHTOP CREB3L4 SLC27A3 ENSG00000272654
GH01J153851 Promoter 0.5 EPDnew 661.3 +71.6 71568 0.1 GATAD2B ENSG00000223599 LOC645965 DENND4B CRTC2 ENSG00000233222 ENSG00000243613 INTS3 MIR190B TPM3
GH01J153961 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.2 -39.9 -39935 4 HDGF PKNOX1 SMAD1 ZFP64 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B CRTC2 SLC39A1 MIR6737 ENSG00000282386 ILF2 CREB3L4 UBAP2L RAB13 RPS27 RPL34P5
GH01J153975 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10.5 -54.1 -54119 3.4 HDGF FOXA2 ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF207 ZNF143 KLF13 JTB GC01P153977 ENSG00000272654 DENND4B GATAD2B CREB3L4 ENSG00000233222 ENSG00000243613 SLC39A1
GH01J153803 Enhancer 1.2 Ensembl ENCODE dbSUPER 11.1 +117.9 117939 4 HDGF PKNOX1 SMAD1 KLF17 STAT5A BMI1 BATF IRF4 ZNF121 ZNF143 CREB3L4 GATAD2B CRTC2 ENSG00000243613 ENSG00000233222 INTS3 NPR1 HAX1 S100A1 LOC105371448
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GATAD2B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GATAD2B gene promoter:

Genomic Locations for GATAD2B Gene

Genomic Locations for GATAD2B Gene
chr1:153,789,030-153,923,360
(GRCh38/hg38)
Size:
134,331 bases
Orientation:
Minus strand
chr1:153,777,201-153,895,451
(GRCh37/hg19)

Genomic View for GATAD2B Gene

Genes around GATAD2B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GATAD2B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GATAD2B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GATAD2B Gene

Proteins for GATAD2B Gene

  • Protein details for GATAD2B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WXI9-P66B_HUMAN
    Recommended name:
    Transcriptional repressor p66-beta
    Protein Accession:
    Q8WXI9
    Secondary Accessions:
    • D3DUZ2
    • Q5VUR2
    • Q7LG68
    • Q9ULS0

    Protein attributes for GATAD2B Gene

    Size:
    593 amino acids
    Molecular mass:
    65261 Da
    Quaternary structure:
    • Binds MBD2 and MBD3. Interaction with MBD2 is required for the enhancement of MBD2-mediated repression and for targeting to the chromatin. Component of the MeCP1 histone deacetylase complex. Interacts with histone tails, including that of histones H2A, H2B, H3 and H4.

neXtProt entry for GATAD2B Gene

Post-translational modifications for GATAD2B Gene

  • Ubiquitination at Lys467 and isoforms=44
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Boster Bio Antibodies for GATAD2B
  • Santa Cruz Biotechnology (SCBT) Antibodies for GATAD2B

No data available for DME Specific Peptides for GATAD2B Gene

Domains & Families for GATAD2B Gene

Gene Families for GATAD2B Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for GATAD2B Gene

Suggested Antigen Peptide Sequences for GATAD2B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8WXI9

UniProtKB/Swiss-Prot:

P66B_HUMAN :
  • Both CR1 and CR2 regions are required for speckled nuclear localization.
Domain:
  • Both CR1 and CR2 regions are required for speckled nuclear localization.
genes like me logo Genes that share domains with GATAD2B: view

Function for GATAD2B Gene

Molecular function for GATAD2B Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor. Enhances MBD2-mediated repression. Efficient repression requires the presence of GATAD2A. Targets MBD3 to discrete loci in the nucleus. May play a role in synapse development.

Phenotypes From GWAS Catalog for GATAD2B Gene

Gene Ontology (GO) - Molecular Function for GATAD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 CONTRIBUTES_TO RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0000978 contributes_to RNA polymerase II proximal promoter sequence-specific DNA binding HDA 16217013
GO:0000980 contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding HDA 16217013
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA --
GO:0003700 DNA binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with GATAD2B: view

Phenotypes for GATAD2B Gene

genes like me logo Genes that share phenotypes with GATAD2B: view

Human Phenotype Ontology for GATAD2B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for GATAD2B Gene

miRTarBase miRNAs that target GATAD2B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for GATAD2B Gene

Localization for GATAD2B Gene

Subcellular locations from UniProtKB/Swiss-Prot for GATAD2B Gene

Nucleus speckle. Note=Speckled nuclear localization requires both CR1 and CR2 regions.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GATAD2B gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for GATAD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin HDA 16217013
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0016581 NuRD complex IBA --
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with GATAD2B: view

Pathways & Interactions for GATAD2B Gene

genes like me logo Genes that share pathways with GATAD2B: view

Gene Ontology (GO) - Biological Process for GATAD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0043044 ATP-dependent chromatin remodeling HDA 16217013
genes like me logo Genes that share ontologies with GATAD2B: view

No data available for SIGNOR curated interactions for GATAD2B Gene

Drugs & Compounds for GATAD2B Gene

No Compound Related Data Available

Transcripts for GATAD2B Gene

mRNA/cDNA for GATAD2B Gene

Unigene Clusters for GATAD2B Gene

GATA zinc finger domain containing 2B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GATAD2B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: -
SP2:

Relevant External Links for GATAD2B Gene

GeneLoc Exon Structure for
GATAD2B
ECgene alternative splicing isoforms for
GATAD2B

Expression for GATAD2B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GATAD2B Gene

Protein differential expression in normal tissues from HIPED for GATAD2B Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (11.1), CD8 Tcells (10.8), and Cervix (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GATAD2B Gene



Protein tissue co-expression partners for GATAD2B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GATAD2B Gene:

GATAD2B

SOURCE GeneReport for Unigene cluster for GATAD2B Gene:

Hs.4779

mRNA Expression by UniProt/SwissProt for GATAD2B Gene:

Q8WXI9-P66B_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for GATAD2B Gene

  • Nervous system(4.5)
  • Liver(4.3)
  • Lung(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GATAD2B Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • face
  • head
  • lip
  • nose
  • skull
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with GATAD2B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for GATAD2B Gene

Orthologs for GATAD2B Gene

This gene was present in the common ancestor of animals.

Orthologs for GATAD2B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GATAD2B 34 33
  • 99.61 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GATAD2B 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia GATAD2B 34 33
  • 94.37 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gatad2b 16 34 33
  • 92.97 (n)
rat
(Rattus norvegicus)
Mammalia Gatad2b 33
  • 92.69 (n)
dog
(Canis familiaris)
Mammalia GATAD2B 34 33
  • 92.52 (n)
OneToOne
chicken
(Gallus gallus)
Aves GATAD2B 34 33
  • 76.76 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GATAD2B 34
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486823 33
  • 72.47 (n)
zebrafish
(Danio rerio)
Actinopterygii gatad2b 33
  • 66.33 (n)
ndufa13 34
  • 26 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta simj 34
  • 20 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea dcp-66 34
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea Cin.3981 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3981 33
Species where no ortholog for GATAD2B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GATAD2B Gene

ENSEMBL:
Gene Tree for GATAD2B (if available)
TreeFam:
Gene Tree for GATAD2B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GATAD2B: view image

Paralogs for GATAD2B Gene

Paralogs for GATAD2B Gene

(1) SIMAP similar genes for GATAD2B Gene using alignment to 1 proteins:

  • P66B_HUMAN
genes like me logo Genes that share paralogs with GATAD2B: view

Variants for GATAD2B Gene

Sequence variations from dbSNP and Humsavar for GATAD2B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1057518674 pathogenic, Mental retardation, autosomal dominant 18 153,818,075(-) G/A coding_sequence_variant, stop_gained
rs1057519401 likely-benign, Mental retardation, autosomal dominant 18 153,816,335(-) T/C coding_sequence_variant, missense_variant
rs115193744 benign, likely-benign, not specified, not provided 153,818,093(-) G/A/C coding_sequence_variant, missense_variant
rs145131801 benign, likely-benign, not specified, not provided 153,812,083(-) G/A coding_sequence_variant, missense_variant
rs587776931 pathogenic, Mental retardation, autosomal dominant 18 153,813,261(-) G/A coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for GATAD2B Gene

Variant ID Type Subtype PubMed ID
esv3578196 CNV loss 25503493
esv3587594 CNV loss 21293372
esv3587595 CNV loss 21293372
esv3587596 CNV loss 21293372
nsv1078969 CNV deletion 25765185
nsv1120199 CNV tandem duplication 24896259
nsv1130976 CNV deletion 24896259
nsv476590 CNV novel sequence insertion 20440878
nsv547941 CNV loss 21841781

Variation tolerance for GATAD2B Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.69; 32.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GATAD2B Gene

Human Gene Mutation Database (HGMD)
GATAD2B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GATAD2B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GATAD2B Gene

Disorders for GATAD2B Gene

MalaCards: The human disease database

(3) MalaCards diseases for GATAD2B Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal dominant 18
  • mrd18
koolen-de vries syndrome
  • kdvs
kleefstra syndrome
  • chromosome 9q34.3 deletion syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

P66B_HUMAN
  • Mental retardation, autosomal dominant 18 (MRD18) [MIM:615074]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD18 patients have severe intellectual disability and dysmorphic features. {ECO:0000269 PubMed:23033978, ECO:0000269 PubMed:23644463}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GATAD2B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GATAD2B: view

No data available for Genatlas for GATAD2B Gene

Publications for GATAD2B Gene

  1. Identification and functional characterization of the p66/p68 components of the MeCP1 complex. (PMID: 11756549) Feng Q … Zhang Y (Molecular and cellular biology 2002) 2 3 4 58
  2. Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PMID: 10574461) Hirosawa M … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  3. GATAD2B loss-of-function mutations cause a recognisable syndrome with intellectual disability and are associated with learning deficits and synaptic undergrowth in Drosophila. (PMID: 23644463) Willemsen MH … Kleefstra T (Journal of medical genetics 2013) 3 4 58
  4. Diagnostic exome sequencing in persons with severe intellectual disability. (PMID: 23033978) de Ligt J … Vissers LE (The New England journal of medicine 2012) 3 4 58
  5. Identification of a linkage disequilibrium block in chromosome 1q associated with BMD in premenopausal white women. (PMID: 18505370) Ichikawa S … Econs MJ (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2008) 3 44 58

Products for GATAD2B Gene

Sources for GATAD2B Gene

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