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MBD3 methyl-CpG binding domain protein 3 [ Homo sapiens (human) ]

Gene ID: 53615, updated on 15-Apr-2019

Summary

Official Symbol
MBD3provided by HGNC
Official Full Name
methyl-CpG binding domain protein 3provided by HGNC
Primary source
HGNC:HGNC:6918
See related
Ensembl:ENSG00000071655 MIM:603573
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
DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in placenta (RPKM 23.4), fat (RPKM 18.3) and 25 other tissues See more
Orthologs

Genomic context

See MBD3 in Genome Data Viewer
Location:
19p13.3
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (1576671..1592761, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1576670..1592760, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene mex-3 RNA binding family member D Neighboring gene RNA, 7SL, cytoplasmic 477, pseudogene Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene RNA, U6 small nuclear 1223, pseudogene Neighboring gene transcription factor 3

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?

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...
  • Cytosine methylation, organism-specific biosystem (from WikiPathways)
    Cytosine methylation, organism-specific biosystemDNA, namely cytosine, methylation is the key event in epigentics. The degree of methylation influences gene expression and methylation disorders are known to be major causes of some diseases like Ret...
  • 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

  • FLJ35189, DKFZp762G113

Gene Ontology Provided by GOA

Process Evidence Code Pubs
ATP-dependent chromatin remodeling HDA PubMed 
aging IEA
Inferred from Electronic Annotation
more info
 
brain development IEA
Inferred from Electronic Annotation
more info
 
embryonic organ development IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
histone acetylation IEA
Inferred from Electronic Annotation
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
methylation-dependent chromatin silencing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of DNA methylation IEA
Inferred from Electronic Annotation
more info
 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to nutrient levels IEA
Inferred from Electronic Annotation
more info
 
tissue development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
NuRD complex NAS
Non-traceable Author Statement
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
heterochromatin IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin HDA PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein-containing complex HDA PubMed 

General protein information

Preferred Names
methyl-CpG-binding domain protein 3

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_029897.2 RefSeqGene

    Range
    4893..20983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001281453.2NP_001268382.1  methyl-CpG-binding domain protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001268382.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC005943
    Consensus CDS
    CCDS12072.1
    UniProtKB/Swiss-Prot
    O95983
    Related
    ENSP00000412302.2, ENST00000434436.8
    Conserved Domains (3) summary
    cd01396
    Location:579
    MeCP2_MBD; MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding ...
    pfam14048
    Location:153243
    MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
    pfam16564
    Location:83148
    MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
  2. NM_001281454.1NP_001268383.1  methyl-CpG-binding domain protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001268383.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
    Source sequence(s)
    AA576859, BC043619, BM684485, BU181763
    Consensus CDS
    CCDS62481.1
    UniProtKB/Swiss-Prot
    O95983
    Related
    ENSP00000156825.2, ENST00000156825.5
    Conserved Domains (3) summary
    pfam14048
    Location:121211
    MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
    pfam16564
    Location:51116
    MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
    cl00110
    Location:547
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

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_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    1576671..1592761 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_003926.5: Suppressed sequence

    Description
    NM_003926.5: This RefSeq was permanently suppressed because currently there is support for the protein but not for the transcript.
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