Format

Send to:

Choose Destination
    • Showing Current items.

    GATAD2B GATA zinc finger domain containing 2B [ Homo sapiens (human) ]

    Gene ID: 57459, updated on 17-Jun-2019

    Summary

    Official Symbol
    GATAD2Bprovided by HGNC
    Official Full Name
    GATA zinc finger domain containing 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:30778
    See related
    Ensembl:ENSG00000143614 MIM:614998
    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
    p68; MRD18; P66beta
    Summary
    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]
    Expression
    Ubiquitous expression in brain (RPKM 8.8), spleen (RPKM 5.8) and 25 other tissues See more
    Orthologs

    Genomic context

    See GATAD2B in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (153804725..153923953, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153777201..153895451, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 27 member 3 Neighboring gene immunoglobulin superfamily DCC subclass member 3 pseudogene Neighboring gene adipose differentiation-related protein pseudogene Neighboring gene uncharacterized LOC101928059 Neighboring gene DENN domain containing 4B Neighboring gene CREB regulated transcription coactivator 2

    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
    Mental retardation, autosomal dominant 18
    MedGen: C3554448 OMIM: 615074 GeneReviews: Not available
    not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2017-12-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2017-12-27)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Genome-wide association identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression, organism-specific biosystem (from REACTOME)
      ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression, organism-specific biosystemAbout half of the rRNA genes in the genome are actively expressed, being transcribed by RNA polymerase I (reviewed in Nemeth and Langst 2008, Bartova et al. 2010, Goodfellow and Zomerdijk 2012, Grumm...
    • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
      Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
      Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
    • HDACs deacetylate histones, organism-specific biosystem (from REACTOME)
      HDACs deacetylate histones, organism-specific biosystemLysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2...
    • Positive epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
      Positive epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in Percipalle and Farrants 2006, McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2...
    • RNA Polymerase I Promoter Clearance, organism-specific biosystem (from REACTOME)
      RNA Polymerase I Promoter Clearance, organism-specific biosystemPromoter clearance is one of the rate-limiting steps in Polymerase I transcription. This step is composed of three phases, promoter opening, transcription initiation and promoter escape.
    • RNA Polymerase I Transcription, organism-specific biosystem (from REACTOME)
      RNA Polymerase I Transcription, organism-specific biosystemThe rRNA genes are transcribed by RNA polymerase I, one of three eukaryotic nuclear RNA polymerases. The polymerase is a multisubunit complex, composed of two large subunits (the most conserved porti...
    • RNA Polymerase I Transcription Initiation, organism-specific biosystem (from REACTOME)
      RNA Polymerase I Transcription Initiation, organism-specific biosystemDuring initiation the double-stranded DNA must be melted and transcription begins. SL1 forms and interacts with UBF-1 and the rDNA promoter. It is this platform that will recruit active RNA polymeras...
    • RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription, organism-specific biosystem (from REACTOME)
      RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription, organism-specific biosystemTranscription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
    • Regulation of TP53 Activity, organism-specific biosystem (from REACTOME)
      Regulation of TP53 Activity, organism-specific biosystemProtein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation,...
    • Regulation of TP53 Activity through Acetylation, organism-specific biosystem (from REACTOME)
      Regulation of TP53 Activity through Acetylation, organism-specific biosystemTranscriptional activity of TP53 is positively regulated by acetylation of several of its lysine residues. BRD7 binds TP53 and promotes acetylation of TP53 lysine residue K382 by acetyltransferase EP...
    • Signaling events mediated by HDAC Class I, organism-specific biosystem (from Pathway Interaction Database)
      Signaling events mediated by HDAC Class I, organism-specific biosystem
      Signaling events mediated by HDAC Class I
    • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
      Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ37346, KIAA1150, MGC138257, MGC138285

    General protein information

    Preferred Names
    transcriptional repressor p66-beta
    Names
    GATA zinc finger domain-containing protein 2B
    transcription repressor p66 beta component of the MeCP1 complex

    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_050988.1 RefSeqGene

      Range
      5001..123069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020699.4NP_065750.1  transcriptional repressor p66-beta

      See identical proteins and their annotated locations for NP_065750.1

      Status: REVIEWED

      Source sequence(s)
      AF411836, AL513523, BQ446626, DA161156
      Consensus CDS
      CCDS1054.1
      UniProtKB/Swiss-Prot
      Q8WXI9
      Related
      ENSP00000357644.4, ENST00000368655.5
      Conserved Domains (2) summary
      pfam00320
      Location:420454
      GATA; GATA zinc finger
      pfam16563
      Location:159194
      P66_CC; Coiled-coil and interaction region of P66A and P66B with MBD2

    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_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      153804725..153923953 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024448621.1XP_024304389.1  transcriptional repressor p66-beta isoform X1

      Conserved Domains (2) summary
      pfam00320
      Location:420454
      GATA; GATA zinc finger
      pfam16563
      Location:159194
      P66_CC; Coiled-coil and interaction region of P66A and P66B with MBD2
    2. XM_005245364.4XP_005245421.1  transcriptional repressor p66-beta isoform X1

      See identical proteins and their annotated locations for XP_005245421.1

      UniProtKB/Swiss-Prot
      Q8WXI9
      Related
      ENSP00000489184.1, ENST00000634544.1
      Conserved Domains (2) summary
      pfam00320
      Location:420454
      GATA; GATA zinc finger
      pfam16563
      Location:159194
      P66_CC; Coiled-coil and interaction region of P66A and P66B with MBD2

    Reference GRCh38.p13 ALT_REF_LOCI_1

    Genomic

    1. NW_003315905.1 Reference GRCh38.p13 ALT_REF_LOCI_1

      Range
      121426..145051 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center