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Aliases for MBD4 Gene

Aliases for MBD4 Gene

  • Methyl-CpG Binding Domain 4, DNA Glycosylase 2 3 5
  • Methyl-CpG Binding Domain Protein 4 2 3
  • Mismatch-Specific DNA N-Glycosylase 3 4
  • Methyl-CpG-Binding Endonuclease 1 3 4
  • Methyl-CpG-Binding Protein MBD4 3 4
  • MED1 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 4, DNA Glycosylase) is a Protein Coding gene. Diseases associated with MBD4 include Classic Rett Syndrome and Rett Syndrome. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and Depyrimidination. 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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MBD4 Gene

Genomics for MBD4 Gene

Regulatory Elements for MBD4 Gene

Enhancers for MBD4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G129223 2 FANTOM5 Ensembl ENCODE dbSUPER 13.6 +210.4 210382 12.0 HDGF PKNOX1 FOXA2 MLX CREB3L1 ARNT ZFP64 SIN3A ARID4B DMAP1 KIAA1257 RAB43 CNBP GP9 ISY1 HMCES MBD4 RPL32P3 ACAD9 POU5F1P6
GH03G129460 1.5 FANTOM5 ENCODE dbSUPER 11.7 -21.9 -21865 2.7 PKNOX1 ATF1 ARID4B FEZF1 TCF12 ZNF121 ZNF766 GLIS2 ELK1 GATA2 RPL32P3 IFT122 MBD4 RHO PIR50923 GC03P129592 GC03P129587
GH03G129525 1.5 FANTOM5 Ensembl ENCODE 10.3 -86.0 -86022 2.0 HDGF ARNT ARID4B SIN3A YY1 ZNF143 ZNF207 FOS DEK REST RPL32P3 IFT122 RHO PLXND1 MBD4 GC03M129503
GH03G129489 1.5 Ensembl ENCODE dbSUPER 10.1 -50.8 -50849 2.9 PKNOX1 MLX ZFP64 ARID4B ZNF2 ZNF48 ZNF143 ZNF207 FOS ZNF263 PLXND1 RPL32P3 IFT122 RHO RNY3P13 MBD4 PIR61564 PIR46036
GH03G129484 1.4 Ensembl ENCODE dbSUPER 10.8 -46.3 -46348 3.8 PKNOX1 NFIB SIN3A RAD21 ZBTB7B YY1 FOS RCOR1 EGR2 HCFC1 RPL32P3 IFT122 ENSG00000244932 H1FX-AS1 RHO PLXND1 MBD4 RNY3P13 PIR40537 PIR61564
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around MBD4 on UCSC Golden Path with GeneCards custom track

Promoters for MBD4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000158230 279 2201 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207

Genomic Location for MBD4 Gene

Chromosome:
3
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

Genes around MBD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MBD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for MBD4 Gene

  • Ubiquitination at Lys484
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for MBD4 Gene

Domains & Families 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

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

No data available for UniProtKB/Swiss-Prot 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 IEA --
GO:0003696 satellite DNA binding TAS 9774669
GO:0003824 catalytic activity IEA --
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

miRNA for MBD4 Gene

miRTarBase miRNAs that target MBD4

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MBD4 Gene

Localization for MBD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD4 Gene

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 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:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with MBD4: view

Pathways & Interactions for MBD4 Gene

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

Pathways by source for MBD4 Gene

Gene Ontology (GO) - Biological Process for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair TAS 10097147
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0032355 response to estradiol IEA --
GO:0045008 depyrimidination TAS --
genes like me logo Genes that share ontologies with MBD4: view

No data available for SIGNOR curated interactions for MBD4 Gene

Drugs & Compounds for MBD4 Gene

(4) Drugs for MBD4 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(9) Additional Compounds for MBD4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for MBD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MBD4 Gene

This gene is overexpressed in Lavage (58.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for MBD4 Gene



NURSA nuclear receptor signaling pathways regulating expression of MBD4 Gene:

MBD4

SOURCE GeneReport for Unigene cluster for MBD4 Gene:

Hs.35947

Evidence on tissue expression from TISSUES for MBD4 Gene

  • Nervous system(4.5)
  • Lung(4.2)
  • Intestine(2.6)
  • Blood(2)
genes like me logo Genes that share expression patterns with MBD4: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 35
  • 99.48 (n)
dog
(Canis familiaris)
Mammalia MBD4 34 35
  • 86.27 (n)
cow
(Bos Taurus)
Mammalia MBD4 34 35
  • 82.85 (n)
mouse
(Mus musculus)
Mammalia Mbd4 34 16 35
  • 78.16 (n)
rat
(Rattus norvegicus)
Mammalia Mbd4 34
  • 77.92 (n)
oppossum
(Monodelphis domestica)
Mammalia MBD4 35
  • 57 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia MBD4 35
  • 43 (a)
OneToOne
chicken
(Gallus gallus)
Aves MBD4 35
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia MBD4 35
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6790 34
zebrafish
(Danio rerio)
Actinopterygii Dr.16765 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 56 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8051 34
Species where no ortholog for MBD4 was found in the sources mined by GeneCards:
  • 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

(1) 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
rs267607193 Pathogenic 129,440,351(+) ACGTG(C/G)AGAGA upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs3138334 Likely benign 129,440,125(-) AGCAA(C/T)GGTGG upstream-variant-2KB, utr-variant-5-prime
rs148987764 Uncertain significance 129,440,121(+) AGTGC(A/C)ACCAT upstream-variant-2KB, utr-variant-5-prime
rs2307293 Uncertain significance 129,431,542(-) ATCAT(C/G)ACTGG reference, missense, utr-variant-3-prime
rs36222038 Uncertain significance 129,440,386(-) CGAAC(A/C)GCCCC intron-variant, upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv2725901 CNV deletion 23290073
esv3597741 CNV loss 21293372
nsv591668 CNV gain 21841781

Variation tolerance for MBD4 Gene

Residual Variation Intolerance Score: 62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.59; 72.38% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for MBD4 Gene

Human Gene Mutation Database (HGMD)
MBD4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MBD4

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

Disorders for MBD4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for MBD4 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
classic rett syndrome
rett syndrome
  • rett syndrome, preserved speech variant
hyperplastic polyposis syndrome
  • serrated polyposis
angelman syndrome
  • happy puppet syndrome
- elite association - COSMIC cancer census association via MalaCards
Search MBD4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for MBD4

Genetic Association Database (GAD)
MBD4
Human Genome Epidemiology (HuGE) Navigator
MBD4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MBD4
genes like me logo Genes that share disorders with MBD4: view

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

Publications for MBD4 Gene

  1. 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 22 64
  2. 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 22 64
  3. Single nucleotide polymorphism in the methyl-CpG binding domain 4 gene and the risk for immune thrombocytopenic purpura in Chinese population. (PMID: 20100009) Zhao H. … Yang R. (Platelets 2010) 3 22 46 64
  4. The Glu346Lys polymorphism and frameshift mutations of the Methyl-CpG Binding Domain 4 gene in gastrointestinal cancer. (PMID: 19469655) Song J.H. … Park W.S. (Neoplasma 2009) 3 22 46 64
  5. Tagging single nucleotide polymorphisms in MBD4 are associated with risk of lung cancer in a Chinese population. (PMID: 18495292) Miao R. … Shen H. (Lung Cancer 2008) 3 22 46 64

Products for MBD4 Gene

  • Addgene plasmids for MBD4

Sources for MBD4 Gene

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