DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA.... See more...

Aliases for MBD2 Gene

Aliases for MBD2 Gene

  • Methyl-CpG Binding Domain Protein 2 2 3 5
  • Methyl-CpG-Binding Domain Protein 2 3 4
  • Demethylase 3 4
  • DMTase 3 4
  • Methyl-CpG-Binding Protein MBD2 4
  • NY-CO-41 3
  • MBD2 5

External Ids for MBD2 Gene

Previous GeneCards Identifiers for MBD2 Gene

  • GC18M051851
  • GC18M051615
  • GC18M049932
  • GC18M049934
  • GC18M048535

Summaries for MBD2 Gene

Entrez Gene Summary for MBD2 Gene

  • DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. The protein encoded by this gene may function as a mediator of the biological consequences of the methylation signal. It is also reported that the this protein functions as a demethylase to activate transcription, as DNA methylation causes gene silencing. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]

GeneCards Summary for MBD2 Gene

MBD2 (Methyl-CpG Binding Domain Protein 2) is a Protein Coding gene. Diseases associated with MBD2 include Cerebellar Ataxia, Deafness, And Narcolepsy, Autosomal Dominant and Dehydrated Hereditary Stomatocytosis 1 With Or Without Pseudohyperkalemia And/Or Perinatal Edema. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Gene Expression. Gene Ontology (GO) annotations related to this gene include chromatin binding and protein domain specific binding. An important paralog of this gene is MBD3.

UniProtKB/Swiss-Prot Summary for MBD2 Gene

  • Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemimethylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Functions as a scaffold protein, targeting GATAD2A and GATAD2B to chromatin to promote repression. May enhance the activation of some unmethylated cAMP-responsive promoters.

Gene Wiki entry for MBD2 Gene

Additional gene information for MBD2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MBD2 Gene

Genomics for MBD2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MBD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J054221 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 611.5 +1.0 1039 3.7 SP1 GATAD2A CTCF TEAD4 PRDM10 ZNF629 RFX1 ZNF692 POLR2A BACH1 MBD2 SNORA37
GH18J054259 Enhancer 1 FANTOM5 ENCODE 15.9 -36.5 -36537 3.5 SP1 BACH1 RELA IKZF2 PKNOX1 EED ARID3A DPF2 RELB EGR1 lnc-POLI-1 POLI MBD2 SNORA37 C18orf54 ENSG00000277324
GH18J054250 Enhancer 1.1 ENCODE CraniofacialAtlas 12.1 -28.2 -28151 5.5 GATAD2A ATF7 TEAD4 REST RFX1 RELA RXRB TCF12 IKZF2 SP1 MG828559 POLI C18orf54 MBD2 SNORA37 STARD6 lnc-POLI-1
GH18J054246 Enhancer 1 ENCODE CraniofacialAtlas dbSUPER 12.2 -22.7 -22690 2.6 ZNF143 TCF12 IKZF2 RCOR1 ZFX ARID3A ELK1 RELB RUNX3 GATAD2B POLI MBD2 SNORA37 C18orf54 STARD6 ENSG00000264296 MG828559 FJ601666-035
GH18J054284 Enhancer 1 Ensembl ENCODE 11.4 -60.5 -60475 2.3 SP1 POLR2A BACH1 RELA TCF12 IKZF2 TRIM22 YY1 PKNOX1 EED NONHSAG023893.2 POLI SNORA37 MBD2 C18orf54 STARD6 piR-39341-173
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MBD2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MBD2

Top Transcription factor binding sites by QIAGEN in the MBD2 gene promoter:
  • AP-1
  • c-Myb
  • GATA-3
  • p53
  • Pax-2
  • Pax-2a
  • S8
  • Sp1
  • YY1

Genomic Locations for MBD2 Gene

Genomic Locations for MBD2 Gene
chr18:54,151,606-54,224,669
(GRCh38/hg38)
Size:
73,064 bases
Orientation:
Minus strand
chr18:51,677,971-51,751,158
(GRCh37/hg19)
Size:
73,188 bases
Orientation:
Minus strand

Genomic View for MBD2 Gene

Genes around MBD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MBD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MBD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MBD2 Gene

Proteins for MBD2 Gene

  • Protein details for MBD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBB5-MBD2_HUMAN
    Recommended name:
    Methyl-CpG-binding domain protein 2
    Protein Accession:
    Q9UBB5
    Secondary Accessions:
    • O95242
    • Q9UIS8

    Protein attributes for MBD2 Gene

    Size:
    411 amino acids
    Molecular mass:
    43255 Da
    Quaternary structure:
    • Heterodimer with MBD3. Component of the MeCP1 complex that contains HDAC1 and HDAC2. Binds DNMT1, MIZF, GPN1, SIN3A, GATAD2A/p66-alpha and GATAD2B/p66-beta. Interacts with DHX9. Interacts with SPHK2 (PubMed:19729656).
    Miscellaneous:
    • [Isoform 3]: Incomplete sequence.

    Three dimensional structures from OCA and Proteopedia for MBD2 Gene

    Alternative splice isoforms for MBD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MBD2 Gene

Post-translational modifications for MBD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for MBD2 Gene

No data available for DME Specific Peptides for MBD2 Gene

Domains & Families for MBD2 Gene

Gene Families for MBD2 Gene

Protein Domains for MBD2 Gene

InterPro:
Blocks:
  • Methyl-CpG binding
ProtoNet:

Suggested Antigen Peptide Sequences for MBD2 Gene

GenScript: Design optimal peptide antigens:
  • Methyl-CpG-binding protein MBD2 (MBD2_HUMAN)
  • Antigen NY-CO-41 (O60535_HUMAN)
genes like me logo Genes that share domains with MBD2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for MBD2 Gene

Function for MBD2 Gene

Molecular function for MBD2 Gene

UniProtKB/Swiss-Prot Function:
Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemimethylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Functions as a scaffold protein, targeting GATAD2A and GATAD2B to chromatin to promote repression. May enhance the activation of some unmethylated cAMP-responsive promoters.
GENATLAS Biochemistry:
methyl-CpG binding protein 2,demethylase,40kDa,binding methylated DNA,histone deacetylase complex,widely expressed,underexpressed at the early stage of colorectal and stomach carcinogenesis

Phenotypes From GWAS Catalog for MBD2 Gene

Gene Ontology (GO) - Molecular Function for MBD2 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:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003696 satellite DNA binding TAS 9774669
GO:0003729 mRNA binding IEA --
genes like me logo Genes that share ontologies with MBD2: view
genes like me logo Genes that share phenotypes with MBD2: view

Animal Models for MBD2 Gene

MGI Knock Outs for MBD2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MBD2 Gene

Localization for MBD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD2 Gene

Nucleus. Note=Nuclear, in discrete foci. Detected at replication foci in late S phase.

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 MBD2 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for MBD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex IEA --
GO:0000785 chromatin IEA --
GO:0000790 nuclear chromatin IDA 23770133
GO:0000792 heterochromatin IEA --
GO:0005634 nucleus TAS,NAS 10441743
genes like me logo Genes that share ontologies with MBD2: view

Pathways & Interactions for MBD2 Gene

genes like me logo Genes that share pathways with MBD2: view

Pathways by source for MBD2 Gene

1 GeneGo (Thomson Reuters) pathway for MBD2 Gene
  • Transcription Sin3 and NuRD in transcription regulation
1 Qiagen pathway for MBD2 Gene
  • DNA Methylation and Transcriptional Repression

SIGNOR curated interactions for MBD2 Gene

Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for MBD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IGI 23770133
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006346 methylation-dependent chromatin silencing IGI 23770133
GO:0007507 heart development IEA --
GO:0007568 aging IEA --
genes like me logo Genes that share ontologies with MBD2: view

Drugs & Compounds for MBD2 Gene

(9) Drugs for MBD2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
cyclic amp Experimental Pharma 0

(9) Additional Compounds for MBD2 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Cytosine
  • 4-amino-2(1H)-Pyrimidinone
  • 4-amino-2-Hydroxypyrimidine
  • C
  • Cyt
  • Cytosin
71-30-7
genes like me logo Genes that share compounds with MBD2: view

Transcripts for MBD2 Gene

mRNA/cDNA for MBD2 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD2

Alternative Splicing Database (ASD) splice patterns (SP) for MBD2 Gene

No ASD Table

Relevant External Links for MBD2 Gene

GeneLoc Exon Structure for
MBD2

Expression for MBD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MBD2 Gene

Protein differential expression in normal tissues from HIPED for MBD2 Gene

This gene is overexpressed in Brain (48.0) and Peripheral blood mononuclear cells (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MBD2 Gene



Protein tissue co-expression partners for MBD2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MBD2

SOURCE GeneReport for Unigene cluster for MBD2 Gene:

Hs.25674

mRNA Expression by UniProt/SwissProt for MBD2 Gene:

Q9UBB5-MBD2_HUMAN
Tissue specificity: Highly expressed in brain, heart, kidney, stomach, testis and placenta.

Evidence on tissue expression from TISSUES for MBD2 Gene

  • Liver(4.4)
  • Skin(2.5)
  • Blood(2.3)
  • Intestine(2.3)
  • Nervous system(2.3)
  • Lymph node(2.3)
  • Kidney(2.2)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with MBD2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for MBD2 Gene

Orthologs for MBD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for MBD2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia MBD2 30 31
  • 98.78 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia MBD2 31
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia MBD2 30 31
  • 96.25 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia MBD2 30 31
  • 93.47 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Mbd2 30 17 31
  • 91.32 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Mbd2 30
  • 89.92 (n)
Oppossum
(Monodelphis domestica)
Mammalia MBD2 31
  • 89 (a)
OneToOne
Chicken
(Gallus gallus)
Aves MBD2 30
  • 69.29 (n)
-- 31
  • 67 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia MBD2 31
  • 92 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.21615 30
Zebrafish
(Danio rerio)
Actinopterygii mbd2 30 31
  • 69.59 (n)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta MBD-like 30 31 32
  • 52.4 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003982 30
  • 50.55 (n)
Species where no ortholog for MBD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for MBD2 Gene

ENSEMBL:
Gene Tree for MBD2 (if available)
TreeFam:
Gene Tree for MBD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MBD2: view image

Paralogs for MBD2 Gene

Paralogs for MBD2 Gene

(2) SIMAP similar genes for MBD2 Gene using alignment to 2 proteins:

  • MBD2_HUMAN
  • J3KSA7_HUMAN
genes like me logo Genes that share paralogs with MBD2: view

Variants for MBD2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MBD2 Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
779981 Benign: not provided 54,164,588(-) A/G SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for MBD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for MBD2 Gene

Variant ID Type Subtype PubMed ID
esv3422299 CNV insertion 20981092
esv993042 CNV deletion 20482838
nsv1072267 CNV deletion 25765185
nsv1121952 CNV deletion 24896259

Variation tolerance for MBD2 Gene

Residual Variation Intolerance Score: 23.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.90; 18.64% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MBD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MBD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MBD2 Gene

Disorders for MBD2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for MBD2 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search MBD2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MBD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with MBD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MBD2 Gene

Publications for MBD2 Gene

  1. 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 4 23
  2. 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 23
  3. p66alpha and p66beta of the Mi-2/NuRD complex mediate MBD2 and histone interaction. (PMID: 16415179) Brackertz M … Renkawitz R (Nucleic acids research 2006) 3 4 23
  4. Genotypes and haplotypes of the methyl-CpG-binding domain 2 modify breast cancer risk dependent upon menopausal status. (PMID: 16168120) Zhu Y … Zheng T (Breast cancer research : BCR 2005) 3 23 41
  5. Antithetic effects of MBD2a on gene regulation. (PMID: 12665568) Fujita H … Nakajima T (Molecular and cellular biology 2003) 3 4 23

Products for MBD2 Gene

Sources for MBD2 Gene