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Aliases for MBD3 Gene

Aliases for MBD3 Gene

  • Methyl-CpG Binding Domain Protein 3 2 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. Diseases associated with MBD3 include cutaneous lupus erythematosus and subacute cutaneous lupus erythematosus. Among its related pathways are Development NOTCH1-mediated pathway for NF-KB activity modulation and Gene Expression. GO annotations related to this gene include chromatin binding. An important paralog of this gene is MBD3L3.

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for MBD3 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Other Protein References for MBD3 Gene

Antibody Products

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

No data available for DME Specific Peptides for MBD3 Gene

Domains 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 :
  • O95983
Domain:
  • Contains 1 MBD (methyl-CpG-binding) domain.
genes like me logo Genes that share domains with MBD3: view

No data available for Gene Families for MBD3 Gene

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.

Gene Ontology (GO) - Molecular Function for MBD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 contributes_to RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 16217013
GO:0000980 contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding IDA 16217013
GO:0003677 DNA binding TAS 9774669
GO:0003682 chromatin binding --
GO:0005488 binding --
genes like me logo Genes that share ontologies with MBD3: view
genes like me logo Genes that share phenotypes with MBD3: view

Animal Model Products

CRISPR Products

miRNA for MBD3 Gene

miRTarBase miRNAs that target MBD3

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for MBD3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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:0000785 chromatin --
GO:0000790 nuclear chromatin IDA 16217013
GO:0000792 heterochromatin IEA --
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with MBD3: view

Pathways for MBD3 Gene

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

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Remodeling Factors in human,mouse,rat

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 IEA --
GO:0001701 in utero embryonic development IEA --
GO:0006325 chromatin organization TAS --
GO:0006346 methylation-dependent chromatin silencing IEA --
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with MBD3: view

Transcripts for MBD3 Gene

Unigene Clusters for MBD3 Gene

Methyl-CpG binding domain protein 3:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for MBD3

Primer 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

Integrated Proteomics: protein expression 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 expressions with MBD3: view

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 35
  • 88.89 (n)
  • 95.67 (a)
MBD3 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia MBD3 35
  • 91.29 (n)
  • 95.53 (a)
MBD3 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Mbd3 35
  • 89.14 (n)
  • 97.75 (a)
Mbd3 16
Mbd3 36
  • 93 (a)
OneToOne
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 Dr.28407 35
mbd3a 35
  • 77.57 (n)
  • 83.46 (a)
mbd3a 36
  • 81 (a)
ManyToMany
mbd3b 36
  • 83 (a)
ManyToMany
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

Selected 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 MAF
rs9585 -- 1,577,118(-) CCAGC(A/G)AGCCC utr-variant-3-prime
rs12884 -- 1,576,925(+) CCATG(C/G)GGGTC utr-variant-3-prime
rs15315 -- 1,576,706(-) CTGAA(G/T)AAAGC utr-variant-3-prime
rs1053151 -- 1,577,209(-) TGCCC(C/T)GAGTG utr-variant-3-prime
rs1053291 -- 1,576,732(-) AGGGA(A/G)CCGTG utr-variant-3-prime

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

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

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

No data available for UniProtKB/Swiss-Prot 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
  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. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. (PMID: 10444591) Zhang Y. … Reinberg D. (Genes Dev. 1999) 3 23
  4. Expression of the genes of methyl-binding domain proteins in human gliomas. (PMID: 11836615) Schlegel J. … Mennel H.D. (Oncol. Rep. 2002) 3 23
  5. MBD3L2 interacts with MBD3 and components of the NuRD complex and can oppose MBD2-MeCP1-mediated methylation silencing. (PMID: 15701600) Jin S.-G. … Pfeifer G.P. (J. Biol. Chem. 2005) 3 23

Products for MBD3 Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Remodeling Factors in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate MBD3
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for MBD3
    • Block miRNA regulation of MBD3 using miScript Target Protectors
    • Addgene plasmids for MBD3

    Sources for MBD3 Gene

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