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Aliases for MBD3 Gene

Aliases for MBD3 Gene

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

External Ids for MBD3 Gene

Previous GeneCards Identifiers for MBD3 Gene

  • GC19M001639
  • GC19M001516
  • GC19M001527
  • GC19M001576
  • GC19M001350

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. 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 chromatin binding and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is MBD2.

UniProtKB/Swiss-Prot 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

Additional gene information for MBD3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MBD3 Gene

Genomics for MBD3 Gene

GeneHancer (GH) Regulatory Elements for MBD3 Gene

Promoters and enhancers for MBD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J001589 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.1 1085 3.9 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF143 PAF1 MBD3 CIRBP LINC01775 C19orf24 LMNB2 ENSG00000261526 SF3A2 ENSG00000267283 GRIN3B TMEM259
GH19J001584 Promoter/Enhancer 0.7 EPDnew ENCODE 650.4 +7.8 7788 0.2 MBD3 GC19M001585 ENSG00000267059
GH19J001582 Promoter 0.5 EPDnew 650.4 +10.2 10161 0.1 GC19M001585 MBD3 ENSG00000267059
GH19J002474 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.3 -884.6 -884622 5.6 CLOCK MLX YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC ZFP41 SSRP1 GADD45B GC19P002477 SF3A2 TCF3 LOC100288123 ZNF77 ZNF554 ENSG00000267139 MBD3 ENSG00000267283
GH19J001382 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 10.4 +208.8 208775 2.2 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NDUFS7 PIR43938 PIR60227 TRN-GTT2-6 TRF-GAA1-6 SF3A2 CIRBP TMEM259 DAZAP1 LOC100288123
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for MBD3 Gene

Genomic Locations for MBD3 Gene
19,206 bases
Minus strand
16,244 bases
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:
    Recommended name:
    Methyl-CpG-binding domain protein 3
    Protein Accession:
    Secondary Accessions:
    • A8K4B7
    • D6W5Z2
    • Q6PIL9
    • Q6PJZ9
    • Q86XF4

    Protein attributes for MBD3 Gene

    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.
    • Sequence=AAH32443.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MBD3 Gene

    Alternative splice isoforms for MBD3 Gene


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:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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: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:0003677 DNA binding TAS 9774669
GO:0003682 chromatin binding IEA --
GO:0004407 histone deacetylase activity TAS --
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 Model Products

  • Taconic Biosciences Mouse Models for MBD3

Clone Products

  • Addgene plasmids 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

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
cytosol 2

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 --
GO:0000790 nuclear chromatin HDA 16217013
GO:0000792 heterochromatin IEA --
GO:0005634 nucleus IEA,IBA --
GO:0005654 nucleoplasm TAS --
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

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 IBA --
GO:0001701 in utero embryonic development IEA --
GO:0006346 methylation-dependent chromatin silencing IEA,IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated 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

Unigene Clusters for MBD3 Gene

Methyl-CpG binding domain protein 3:
Representative Sequences:

Clone Products

  • Addgene plasmids 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: -
SP8: - - - -

Relevant External Links for MBD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MBD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of MBD3 Gene:


SOURCE GeneReport for Unigene cluster for MBD3 Gene:


Evidence on tissue expression from TISSUES for MBD3 Gene

  • Nervous system(4.8)
  • Muscle(4.3)
  • Lung(2.4)
genes like me logo Genes that share expression patterns with MBD3: view

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
(Pan troglodytes)
Mammalia MBD3 34 33
  • 99.66 (n)
(Canis familiaris)
Mammalia MBD3 34 33
  • 91.29 (n)
(Rattus norvegicus)
Mammalia Mbd3 33
  • 90.51 (n)
(Mus musculus)
Mammalia Mbd3 16 34 33
  • 89.14 (n)
(Bos Taurus)
Mammalia MBD3 34 33
  • 88.89 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 63 (a)
(Gallus gallus)
Aves MBD3 33
  • 82.37 (n)
-- 34
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia mbd3 33
  • 76.77 (n)
Str.6166 33
African clawed frog
(Xenopus laevis)
Amphibia MBD3 33
(Danio rerio)
Actinopterygii mbd3b 34
  • 83 (a)
mbd3a 34 33
  • 77.57 (n)
Dr.28407 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2845 33
fruit fly
(Drosophila melanogaster)
Insecta MBD-like 34
  • 22 (a)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.12343 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12343 33
Species where no ortholog for MBD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

Gene Tree for MBD3 (if available)
Gene Tree for MBD3 (if available)
Evolutionary constrained regions (ECRs) for MBD3: view image

Paralogs for MBD3 Gene

Paralogs for MBD3 Gene

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

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

Variants for MBD3 Gene

Sequence variations from dbSNP and Humsavar for MBD3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000017302 -- 1,581,573(-) G/C intron_variant
rs1000038261 -- 1,576,332(-) G/A downstream_transcript_variant
rs1000069712 -- 1,581,734(-) C/G intron_variant
rs1000169938 -- 1,588,208(-) C/T intron_variant
rs1000257214 -- 1,591,595(-) C/T intron_variant

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for MBD3 Gene

Additional Disease Information for MBD3

No disorders were found for MBD3 Gene.

No data available for MalaCards , 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 58
  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 58
  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 58
  4. MBD3 localizes at promoters, gene bodies and enhancers of active genes. (PMID: 24385926) Shimbo T … Wade PA (PLoS genetics 2013) 3 4 58
  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 58

Products for MBD3 Gene

Sources for MBD3 Gene

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