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Aliases for MBD3 Gene

Aliases for MBD3 Gene

  • Methyl-CpG Binding Domain Protein 3 2 3 5
  • 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. Diseases associated with MBD3 include subacute cutaneous lupus erythematosus and silver-russell syndrome. Among its related pathways are Gene Expression and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include chromatin binding and RNA polymerase II core promoter proximal region 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

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

Genomics for MBD3 Gene

Regulatory Elements for MBD3 Gene

Promoters for MBD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around MBD3 on UCSC Golden Path with GeneCards custom track

Genomic Location for MBD3 Gene

Chromosome:
19
Start:
1,573,596 bp from pter
End:
1,592,801 bp from pter
Size:
19,206 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=Translation N-terminally shortened.; 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

Proteomics data for MBD3 Gene at MOPED

Post-translational modifications for MBD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for MBD3 (MBD3)

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

O95983

UniProtKB/Swiss-Prot:

MBD3_HUMAN :
  • Contains 1 MBD (methyl-CpG-binding) domain.
Domain:
  • Contains 1 MBD (methyl-CpG-binding) domain.
genes like me logo Genes that share domains with MBD3: view

Function for MBD3 Gene

Molecular function for MBD3 Gene

GENATLAS Biochemistry:
methyl-CpG binding protein 3,expressed in somatic tissues,not binding methylated DNA in vitro or in vivo
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.
genes like me logo Genes that share phenotypes with MBD3: view

Animal Models for MBD3 Gene

MGI Knock Outs for MBD3:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for MBD3 Gene COMPARTMENTS Subcellular localization image for MBD3 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for MBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm 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

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 from RNA polymerase II promoter IBA --
GO:0006346 methylation-dependent chromatin silencing IEA,IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0007568 aging IEA --
GO:0016573 histone acetylation 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

Unigene Clusters for MBD3 Gene

Methyl-CpG binding domain protein 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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
ECgene alternative splicing isoforms for
MBD3

Expression for MBD3 Gene

mRNA expression in normal human tissues 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, PaxDb, MOPED, and MaxQB for MBD3 Gene



SOURCE GeneReport for Unigene cluster for MBD3 Gene Hs.178728

genes like me logo Genes that share expression patterns with MBD3: view

Protein tissue co-expression partners for MBD3 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 35
  • 99.66 (n)
  • 100 (a)
MBD3 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia MBD3 36
  • 93 (a)
OneToOne
MBD3 35
  • 88.89 (n)
  • 95.67 (a)
dog
(Canis familiaris)
Mammalia MBD3 35
  • 91.29 (n)
  • 95.53 (a)
MBD3 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Mbd3 36
  • 93 (a)
OneToOne
Mbd3 16
Mbd3 35
  • 89.14 (n)
  • 97.75 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 63 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Mbd3 35
  • 90.51 (n)
  • 97.75 (a)
chicken
(Gallus gallus)
Aves -- 36
  • 61 (a)
ManyToMany
MBD3 35
  • 82.37 (n)
  • 96.15 (a)
African clawed frog
(Xenopus laevis)
Amphibia MBD3 35
tropical clawed frog
(Silurana tropicalis)
Amphibia mbd3 35
  • 76.77 (n)
  • 91.29 (a)
Str.6166 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2845 35
zebrafish
(Danio rerio)
Actinopterygii mbd3a 36
  • 81 (a)
ManyToMany
mbd3b 36
  • 83 (a)
ManyToMany
Dr.28407 35
mbd3a 35
  • 77.57 (n)
  • 83.46 (a)
fruit fly
(Drosophila melanogaster)
Insecta MBD-like 36
  • 22 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12343 35
Species with no ortholog for MBD3:
  • 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

ENSEMBL:
Gene Tree for MBD3 (if available)
TreeFam:
Gene Tree for MBD3 (if available)

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 Sequence Context AA Info Type
rs9585 -- 1,577,118(-) CCAGC(A/G)AGCCC utr-variant-3-prime
rs1060801 -- 1,587,774(-) GGTAC(C/G/T)TGGCC intron-variant
rs1132740 -- 1,576,699(-) AAGCC(A/C)CCATG utr-variant-3-prime
rs1137901 -- 1,587,619(-) tgggc(A/G)acata intron-variant
rs1137902 -- 1,587,590(-) aaaaa(A/G)tttaa intron-variant

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

Variant ID Type Subtype PubMed ID
nsv910292 CNV Loss 21882294
dgv3583n71 CNV Loss 21882294
dgv3589n71 CNV Loss 21882294
esv32942 CNV Gain+Loss 17666407
nsv910499 CNV Loss 21882294
dgv3601n71 CNV Loss 21882294
dgv3602n71 CNV Loss 21882294
dgv3603n71 CNV Loss 21882294
dgv3607n71 CNV Loss 21882294
dgv3608n71 CNV Loss 21882294
dgv3609n71 CNV Loss 21882294
nsv910532 CNV Loss 21882294
dgv3610n71 CNV Loss 21882294
nsv910540 CNV Loss 21882294
nsv828378 CNV Gain 20364138
dgv3611n71 CNV Loss 21882294

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)

Relevant External Links for MBD3 Gene

HapMap Linkage Disequilibrium report
MBD3
Human Gene Mutation Database (HGMD)
MBD3

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

Disorders for MBD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for MBD3 Gene - From: GeneCards

Disorder Aliases PubMed IDs
subacute cutaneous lupus erythematosus
  • lupus erythematosus, subacute cutaneous
silver-russell syndrome
  • silver russell dwarfism
- elite association - COSMIC cancer census association via MalaCards
Search MBD3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for MBD3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (Mol. Cell. Biol. 1998) 2 3 4 23 67
  2. Genomic structure and chromosomal mapping of the murine and human mbd1, mbd2, mbd3, and mbd4 genes. (PMID: 10441743) Hendrich B. … Bird A. (Mamm. Genome 1999) 2 3 23
  3. MBD3 mutations are not responsible for ICR1 hypomethylation in Silver-Russell syndrome. (PMID: 20004753) Bachmann N. … Eggermann T. (Eur J Med Genet 2010) 3 23
  4. A novel role for methyl CpG-binding domain protein 3, a component of the histone deacetylase complex, in regulation of cell cycle progression and cell death. (PMID: 19041848) Noh E.J. … Lee J.S. (Biochem. Biophys. Res. Commun. 2009) 3 23
  5. DNA demethylation induced by the methyl-CpG-binding domain protein MBD3. (PMID: 18602768) Brown S.E. … Szyf M. (Gene 2008) 3 23

Products for MBD3 Gene

Sources for MBD3 Gene

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