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 activiti... See more...

Aliases for MBD3 Gene

Aliases for MBD3 Gene

  • Methyl-CpG Binding Domain Protein 3 2 3 5
  • Methyl-CpG-Binding Domain Protein 3 3 4
  • Methyl-CpG-Binding Protein MBD3 4
  • MBD3 5

External Ids for MBD3 Gene

Previous GeneCards Identifiers for MBD3 Gene

  • GC19M001639
  • GC19M001516
  • GC19M001527
  • GC19M001576
  • GC19M001350
  • GC19M001584
  • GC19M001626
  • GC19M001690
  • GC19M001750
  • GC19M001869

Summaries for MBD3 Gene

Entrez Gene Summary for MBD3 Gene

  • 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]

GeneCards Summary for MBD3 Gene

MBD3 (Methyl-CpG Binding Domain Protein 3) is a Protein Coding gene. Diseases associated with MBD3 include Neuropathy, Hereditary Sensory, Type Ie. Among its related pathways are Chromatin organization and Macrophage Differentiation and Growth Inhibition by METS. Gene Ontology (GO) annotations related to this gene include chromatin binding and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is MBD2.

UniProtKB/Swiss-Prot Summary for MBD3 Gene

  • Acts as transcriptional repressor and plays a role in gene silencing. Does not bind to DNA by itself (PubMed:12124384). Binds to DNA with a preference for sites containing methylated CpG dinucleotides (in vitro). Binds to a lesser degree DNA containing unmethylated CpG dinucleotides (PubMed:24307175). Recruits histone deacetylases and DNA methyltransferases.

Gene Wiki entry for MBD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MBD3 Gene

Genomics for MBD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MBD3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MBD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MBD3

Top Transcription factor binding sites by QIAGEN in the MBD3 gene promoter:
  • c-Myb
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • Egr-4
  • Elk-1
  • RP58
  • STAT3
  • XBP-1

Genomic Locations for MBD3 Gene

Latest Assembly
chr19:1,573,596-1,592,865
(GRCh38/hg38)
Size:
19,270 bases
Orientation:
Minus strand

Previous Assembly
chr19:1,573,595-1,592,864
(GRCh37/hg19 by Entrez Gene)
Size:
19,270 bases
Orientation:
Minus strand

chr19:1,576,639-1,592,882
(GRCh37/hg19 by Ensembl)
Size:
16,244 bases
Orientation:
Minus strand

Genomic View for MBD3 Gene

Genes around MBD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MBD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MBD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MBD3 Gene

Proteins for MBD3 Gene

  • Protein details for MBD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95983-MBD3_HUMAN
    Recommended name:
    Methyl-CpG-binding domain protein 3
    Protein Accession:
    O95983
    Secondary Accessions:
    • A8K4B7
    • D6W5Z2
    • Q6PIL9
    • Q6PJZ9
    • Q86XF4

    Protein attributes for MBD3 Gene

    Size:
    291 amino acids
    Molecular mass:
    32844 Da
    Quaternary structure:
    • Heterodimer with MBD2. Part of the NuRD and the MeCP1 complex. Interacts with BCL6, HDAC1, MTA2, DNMT1, p66-alpha and p66-beta.
    SequenceCaution:
    • Sequence=AAH32443.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MBD3 Gene

    Alternative splice isoforms for MBD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MBD3 Gene

Post-translational modifications for MBD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MBD3 Gene

Domains & Families for MBD3 Gene

Gene Families for MBD3 Gene

Protein Domains for MBD3 Gene

Suggested Antigen Peptide Sequences for MBD3 Gene

GenScript: Design optimal peptide antigens:
  • Methyl-CpG-binding protein MBD3 (MBD3_HUMAN)
genes like me logo Genes that share domains with MBD3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for MBD3 Gene

Function for MBD3 Gene

Molecular function for MBD3 Gene

UniProtKB/Swiss-Prot Function:
Acts as transcriptional repressor and plays a role in gene silencing. Does not bind to DNA by itself (PubMed:12124384). Binds to DNA with a preference for sites containing methylated CpG dinucleotides (in vitro). Binds to a lesser degree DNA containing unmethylated CpG dinucleotides (PubMed:24307175). Recruits histone deacetylases and DNA methyltransferases.
GENATLAS Biochemistry:
methyl-CpG binding protein 3,expressed in somatic tissues,not binding methylated DNA in vitro or in vivo

Gene Ontology (GO) - Molecular Function for MBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 9774669
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 12183469
GO:0008327 methyl-CpG binding IEA,IDA 24307175
GO:0031492 contributes_to nucleosomal DNA binding HDA 16217013
genes like me logo Genes that share ontologies with MBD3: view
genes like me logo Genes that share phenotypes with MBD3: view

Animal Models for MBD3 Gene

MGI Knock Outs for MBD3:

Animal Models for research

  • Taconic Biosciences Mouse Models for MBD3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MBD3 Gene

Localization for MBD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD3 Gene

Nucleus. Chromosome. Note=Nuclear, in discrete foci. Detected on chromatin, at promoter regions of active genes.

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 MBD3 gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for MBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IEA,HDA 16217013
GO:0000792 heterochromatin IEA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with MBD3: view

Pathways & Interactions for MBD3 Gene

genes like me logo Genes that share pathways with MBD3: view

Pathways by source for MBD3 Gene

1 GeneGo (Thomson Reuters) pathway for MBD3 Gene
  • Transcription Sin3 and NuRD in transcription regulation
1 Qiagen pathway for MBD3 Gene
  • DNA Methylation and Transcriptional Repression
1 Cell Signaling Technology pathway for MBD3 Gene

SIGNOR curated interactions for MBD3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for MBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001701 in utero embryonic development IEA --
GO:0006346 methylation-dependent chromatin silencing IEA --
GO:0007420 brain development IEA --
GO:0007507 heart development IEA --
genes like me logo Genes that share ontologies with MBD3: view

Drugs & Compounds for MBD3 Gene

No Compound Related Data Available

Transcripts for MBD3 Gene

mRNA/cDNA for MBD3 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD3

Alternative Splicing Database (ASD) splice patterns (SP) for MBD3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b · 9c
SP1: - - - - - - -
SP2: - - - - - -
SP3: - -
SP4: - -
SP5: - - - - -
SP6: -
SP7:
SP8: - - - -

Relevant External Links for MBD3 Gene

GeneLoc Exon Structure for
MBD3

Expression for MBD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MBD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MBD3 Gene

This gene is overexpressed in Pancreas (12.8), Peripheral blood mononuclear cells (9.7), and Breast (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MBD3 Gene



Protein tissue co-expression partners for MBD3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MBD3

SOURCE GeneReport for Unigene cluster for MBD3 Gene:

Hs.178728

Evidence on tissue expression from TISSUES for MBD3 Gene

  • Nervous system(4.9)
  • Muscle(4.4)
  • Lung(2.4)
  • Skin(2.3)
genes like me logo Genes that share expression patterns with MBD3: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for MBD3 Gene

Orthologs for MBD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for MBD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia MBD3 29 30
  • 99.66 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia MBD3 29 30
  • 91.29 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Mbd3 29
  • 90.51 (n)
Mouse
(Mus musculus)
Mammalia Mbd3 29 16 30
  • 89.14 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia MBD3 29 30
  • 88.89 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 63 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves MBD3 29
  • 82.37 (n)
-- 30
  • 61 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia mbd3 29
  • 76.77 (n)
Str.6166 29
African clawed frog
(Xenopus laevis)
Amphibia MBD3 29
Zebrafish
(Danio rerio)
Actinopterygii mbd3b 30
  • 83 (a)
ManyToMany
mbd3a 29 30
  • 77.57 (n)
ManyToMany
Dr.28407 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2845 29
Fruit Fly
(Drosophila melanogaster)
Insecta MBD-like 30
  • 22 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.12343 29
Species where no ortholog for MBD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for MBD3 Gene

ENSEMBL:
Gene Tree for MBD3 (if available)
TreeFam:
Gene Tree for MBD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MBD3: view image
Alliance of Genome Resources:
Additional Orthologs for MBD3

Paralogs for MBD3 Gene

Paralogs for MBD3 Gene

(6) SIMAP similar genes for MBD3 Gene using alignment to 2 proteins:

  • MBD3_HUMAN
  • K7EIE8_HUMAN
genes like me logo Genes that share paralogs with MBD3: view

Variants for MBD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MBD3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs111228603 Benign: not provided 1,584,672(-) C/T
NM_001281453.2(MBD3):c.276G>A (p.Lys92=)
SYNONYMOUS
rs139676994 Likely Benign: not provided 1,592,608(-) G/A
NM_001281453.2(MBD3):c.24C>T (p.Cys8=)
SYNONYMOUS_VARIANT,INTRON
rs149679096 Likely Benign: not provided 1,581,178(-) C/T
NM_001281453.2(MBD3):c.591G>A (p.Ser197=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for MBD3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for MBD3 Gene

Variant ID Type Subtype PubMed ID
dgv6203n54 CNV gain 21841781
esv32942 CNV gain+loss 17666407
nsv1138647 CNV deletion 24896259
nsv578312 CNV loss 21841781
nsv828378 CNV gain 20364138
nsv953942 CNV deletion 24416366

Variation tolerance for MBD3 Gene

Residual Variation Intolerance Score: 5.07% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.54; 11.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MBD3 Gene

Human Gene Mutation Database (HGMD)
MBD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MBD3
Leiden Open Variation Database (LOVD)
MBD3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MBD3 Gene

Disorders for MBD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for MBD3 Gene - From: COP

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory, type ie
  • hsn1e
- elite association - COSMIC cancer census association via MalaCards
Search MBD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MBD3

genes like me logo Genes that share disorders with MBD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MBD3 Gene

Publications for MBD3 Gene

  1. Identification and characterization of a family of mammalian methyl-CpG binding proteins. (PMID: 9774669) Hendrich B … Bird A (Molecular and cellular biology 1998) 2 3 4 22
  2. Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and Mbd4 genes. (PMID: 10441743) Hendrich B … Bird A (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 2 3 22
  3. Probing the dynamic distribution of bound states for methylcytosine-binding domains on DNA. (PMID: 24307175) Cramer JM … Williams DC (The Journal of biological chemistry 2014) 3 4
  4. MBD3 localizes at promoters, gene bodies and enhancers of active genes. (PMID: 24385926) Shimbo T … Wade PA (PLoS genetics 2013) 3 4
  5. Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences. (PMID: 23361464) Günther K … Renkawitz R (Nucleic acids research 2013) 3 4

Products for MBD3 Gene

Sources for MBD3 Gene