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Aliases for MBD4 Gene

Aliases for MBD4 Gene

  • Methyl-CpG Binding Domain Protein 4 2 3
  • MED1 3 4 6
  • Mismatch-Specific DNA N-Glycosylase 3 4
  • Methyl-CpG-Binding Endonuclease 1 3 4
  • Methyl-CpG-Binding Protein MBD4 3 4
  • G/5-Fluorouracil Mismatch Glycosylase With Biphasic Kinetics 3
  • Methyl-CpG-Binding Domain Protein 4 3
  • Putative Methyl-CpG Binding Protein 3
  • 3,N(4)-Ethenocytosine Glycosylase 3
  • G/T Mismatch Glycosylase 3
  • G/U Mismatch Glycosylase 3
  • EC 3.2.2.- 4

External Ids for MBD4 Gene

Previous GeneCards Identifiers for MBD4 Gene

  • GC03M125975
  • GC03M129786
  • GC03M130431
  • GC03M130470
  • GC03M130632
  • GC03M129149
  • GC03M126533

Summaries for MBD4 Gene

Entrez Gene Summary for MBD4 Gene

  • The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]

GeneCards Summary for MBD4 Gene

MBD4 (Methyl-CpG Binding Domain Protein 4) is a Protein Coding gene. Diseases associated with MBD4 include 2q23.1 microdeletion syndrome and classic rett syndrome. Among its related pathways are L1CAM interactions and Metabolism. GO annotations related to this gene include endodeoxyribonuclease activity and pyrimidine-specific mismatch base pair DNA N-glycosylase activity. An important paralog of this gene is MECP2.

UniProtKB/Swiss-Prot for MBD4 Gene

  • Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.

Gene Wiki entry for MBD4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MBD4 Gene

Genomics for MBD4 Gene

Regulatory Elements for MBD4 Gene

Epigenetics Products

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

Genomic Location for MBD4 Gene

Start:
129,430,944 bp from pter
End:
129,440,179 bp from pter
Size:
9,236 bases
Orientation:
Minus strand

Genomic View for MBD4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for MBD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MBD4 Gene

Proteins for MBD4 Gene

  • Protein details for MBD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95243-MBD4_HUMAN
    Recommended name:
    Methyl-CpG-binding domain protein 4
    Protein Accession:
    O95243
    Secondary Accessions:
    • B4DZN2
    • D3DNC3
    • D3DNC4
    • E9PEE4
    • Q2MD36
    • Q7Z4T3
    • Q96F09

    Protein attributes for MBD4 Gene

    Size:
    580 amino acids
    Molecular mass:
    66051 Da
    Quaternary structure:
    • Interacts with MLH1.

    Three dimensional structures from OCA and Proteopedia for MBD4 Gene

    Alternative splice isoforms for MBD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MBD4 Gene

Proteomics data for MBD4 Gene at MOPED

Post-translational modifications for MBD4 Gene

  • Ubiquitination at Lys484
  • Modification sites at PhosphoSitePlus

Other Protein References for MBD4 Gene

No data available for DME Specific Peptides for MBD4 Gene

Domains for MBD4 Gene

Protein Domains for MBD4 Gene

Suggested Antigen Peptide Sequences for MBD4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O95243

UniProtKB/Swiss-Prot:

MBD4_HUMAN :
  • O95243
Domain:
  • Contains 1 MBD (methyl-CpG-binding) domain.
genes like me logo Genes that share domains with MBD4: view

No data available for Gene Families for MBD4 Gene

Function for MBD4 Gene

Molecular function for MBD4 Gene

GENATLAS Biochemistry: methyl-CpG binding protein 4,widely expressed,mutated in carcinoma with microsatellite instability (colorectal carcinoma),encoding an MLH1 interactor
UniProtKB/Swiss-Prot Function: Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.

Enzyme Numbers (IUBMB) for MBD4 Gene

Gene Ontology (GO) - Molecular Function for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003696 satellite DNA binding TAS 9774669
GO:0003824 catalytic activity --
GO:0004520 endodeoxyribonuclease activity TAS 10097147
GO:0005515 protein binding IPI 12702765
genes like me logo Genes that share ontologies with MBD4: view
genes like me logo Genes that share phenotypes with MBD4: view

Animal Models for MBD4 Gene

MGI Knock Outs for MBD4:

Animal Model Products

CRISPR Products

No data available for Transcription Factor Targeting and HOMER Transcription for MBD4 Gene

Localization for MBD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD4 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for MBD4 Gene COMPARTMENTS Subcellular localization image for MBD4 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus TAS 9774669
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with MBD4: view

Pathways for MBD4 Gene

genes like me logo Genes that share pathways with MBD4: view

PCR Array Products

Gene Ontology (GO) - Biological Process for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000737 DNA catabolic process, endonucleolytic --
GO:0006281 DNA repair TAS --
GO:0006284 base-excision repair TAS --
GO:0006285 base-excision repair, AP site formation TAS --
GO:0006974 cellular response to DNA damage stimulus --
genes like me logo Genes that share ontologies with MBD4: view

Compounds for MBD4 Gene

(13) Novoseek inferred chemical compound relationships for MBD4 Gene

Compound -log(P) Hits PubMed IDs
5-methylcytosine 77.9 12
thymine 68.5 14
cytosine 68.5 1
3,n(4)-ethenocytosine 66.3 2
5-aza-2deoxycytidine 55.6 1
genes like me logo Genes that share compounds with MBD4: view

Transcripts for MBD4 Gene

Unigene Clusters for MBD4 Gene

Methyl-CpG binding domain protein 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for MBD4

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for MBD4

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for MBD4 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c · 2d ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8a · 8b · 8c · 8d
SP1: - - -
SP2: - - - - -
SP3: - - - -
SP4: - - - - -
SP5: - - - - - - - - - - - -
SP6: - - -
SP7: -
SP8:
SP9: -
SP10:

Relevant External Links for MBD4 Gene

GeneLoc Exon Structure for
MBD4
ECgene alternative splicing isoforms for
MBD4

Expression for MBD4 Gene

mRNA expression in normal human tissues for MBD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for MBD4 Gene

SOURCE GeneReport for Unigene cluster for MBD4 Gene Hs.35947

genes like me logo Genes that share expressions with MBD4: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for MBD4 Gene

Orthologs for MBD4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for MBD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia MBD4 35
  • 99.48 (n)
  • 99.48 (a)
MBD4 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia MBD4 35
  • 82.85 (n)
  • 75.27 (a)
MBD4 36
  • 72 (a)
OneToOne
dog
(Canis familiaris)
Mammalia MBD4 35
  • 86.27 (n)
  • 78.35 (a)
MBD4 36
  • 78 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Mbd4 35
  • 78.16 (n)
  • 68.77 (a)
Mbd4 16
Mbd4 36
  • 65 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia MBD4 36
  • 57 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia MBD4 36
  • 43 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Mbd4 35
  • 77.92 (n)
  • 68.21 (a)
chicken
(Gallus gallus)
Aves MBD4 36
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia MBD4 36
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6790 35
zebrafish
(Danio rerio)
Actinopterygii Dr.16765 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8051 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 56 (a)
OneToMany
Species with no ortholog for MBD4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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 MBD4 Gene

ENSEMBL:
Gene Tree for MBD4 (if available)
TreeFam:
Gene Tree for MBD4 (if available)

Paralogs for MBD4 Gene

Paralogs for MBD4 Gene

Selected SIMAP similar genes for MBD4 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with MBD4: view

Variants for MBD4 Gene

Sequence variations from dbSNP and Humsavar for MBD4 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs10342 -, - 129,436,827(-) CAGAT(A/G/T)CTGAA missense, reference, intron-variant
rs140692 -- 129,437,693(-) GATAG(C/T)ACAGC intron-variant
rs140693 - 129,436,608(-) ACAAC(A/G)AGAAG missense, reference, intron-variant
rs140694 -- 129,434,193(-) TCCCT(C/G)AATAT intron-variant
rs140695 -- 129,433,301(-) TGAAC(A/G)TGAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for MBD4 Gene

Variant ID Type Subtype PubMed ID
nsv877475 CNV Gain 21882294
esv2725901 CNV Deletion 23290073
nsv877476 CNV Gain 21882294
nsv877477 CNV Gain 21882294

Relevant External Links for MBD4 Gene

HapMap Linkage Disequilibrium report
MBD4
Human Gene Mutation Database (HGMD)
MBD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MBD4 Gene

Disorders for MBD4 Gene

(21) Novoseek inferred disease relationships for MBD4 Gene

Disease -log(P) Hits PubMed IDs
rett syndrome 89.6 20
microsatellite instability 69.3 9
mental retardation 47.9 3
angelman syndrome 44.7 2
somatic mutations 39 1

Relevant External Links for MBD4

Genetic Association Database (GAD)
MBD4
Human Genome Epidemiology (HuGE) Navigator
MBD4
genes like me logo Genes that share disorders with MBD4: view

No data available for UniProtKB/Swiss-Prot for MBD4 Gene

Publications for MBD4 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. MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. (PMID: 10097147) Bellacosa A. … Neri G. (Proc. Natl. Acad. Sci. U.S.A. 1999) 2 3 4 23
  3. 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) 3 4 23
  4. Fas-associated death domain protein interacts with methyl-CpG binding domain protein 4: a potential link between genome surveillance and apoptosis. (PMID: 12702765) Screaton R.A. … Frisch S.M. (Proc. Natl. Acad. Sci. U.S.A. 2003) 3 4 23
  5. Biphasic kinetics of the human DNA repair protein MED1 (MBD4), a mismatch-specific DNA N-glycosylase. (PMID: 10930409) Petronzelli F. … Bellacosa A. (J. Biol. Chem. 2000) 3 4 23

Products for MBD4 Gene

  • Addgene plasmids for MBD4

Sources for MBD4 Gene

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