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Aliases for MBD4 Gene

Aliases for MBD4 Gene

  • Methyl-CpG Binding Domain 4, DNA Glycosylase 2 3 5
  • Mismatch-Specific DNA N-Glycosylase 3 4
  • Methyl-CpG Binding Domain Protein 4 2 3
  • 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 Rett Syndrome and Cranioectodermal Dysplasia 1. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and Recognition and association of DNA glycosylase with site containing an affected pyrimidine. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for MBD4 Gene

Promoters and enhancers for MBD4 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
GH03J129438 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.5 -543 4.5 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B IFT122 MBD4 RPL32P3 PLXND1 RHO GC03P129881 GC03P129876 PIR50923
GH03J129591 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.9 -160.8 -160795 19.4 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A YBX1 FEZF1 DMAP1 PLXND1 ENSG00000244932 RPL32P3 ISY1 MBD4 RPS15AP16 ACAD9 RPN1 RHO H1FX-AS1
GH03J129277 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 16.7 +161.0 160985 3.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A YY1 POLR2B E2F8 PAF1 SP3 HMCES RPL32P3 ENSG00000244932 ISY1 MBD4 H1FX RPS15AP16 H1FX-AS1 CNBP COPG1
GH03J129178 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 14.1 +257.6 257635 8.4 PKNOX1 SMAD1 FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 LOC105374101 CNBP RPL32P3 ENSG00000244932 ISY1 H1FX-AS1 MBD4 RPS15AP16 H1FX COPG1
GH03J129398 Promoter/Enhancer 1.5 Ensembl ENCODE 21.4 +40.9 40906 2.2 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 RPL32P3 SNORA7B GC03M129400 ISY1 MBD4 ENSG00000244932 IFT122 H1FX RHO CNBP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MBD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MBD4 gene promoter:
  • Pax-3
  • Nkx2-5
  • GATA-1
  • C/EBPalpha
  • AP-4
  • AML1a
  • Pbx1a
  • RSRFC4
  • deltaCREB

Genomic Locations for MBD4 Gene

Genomic Locations for MBD4 Gene
chr3:129,430,944-129,440,179
(GRCh38/hg38)
Size:
9,236 bases
Orientation:
Minus strand
chr3:129,149,787-129,158,878
(GRCh37/hg19)
Size:
9,092 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 isoforms=2, 3, 6, 5484
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for MBD4

No data available for DME Specific Peptides for MBD4 Gene

Domains & Families for MBD4 Gene

Gene Families for MBD4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

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

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.
GENATLAS Biochemistry:
methyl-CpG binding protein 4,widely expressed,mutated in carcinoma with microsatellite instability (colorectal carcinoma),encoding an MLH1 interactor

Enzyme Numbers (IUBMB) for MBD4 Gene

Phenotypes From GWAS Catalog for MBD4 Gene

Gene Ontology (GO) - Molecular Function for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA,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

miRNA for MBD4 Gene

miRTarBase miRNAs that target MBD4

Clone Products

  • Addgene plasmids for MBD4

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

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:0009314 response to radiation IBA --
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:

Clone Products

  • Addgene plasmids for MBD4

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, 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(2.5)
  • Blood(2)
genes like me logo Genes that share expression patterns with MBD4: view

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 33
  • 99.48 (n)
OneToOne
dog
(Canis familiaris)
Mammalia MBD4 34 33
  • 86.27 (n)
OneToOne
cow
(Bos Taurus)
Mammalia MBD4 34 33
  • 82.85 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Mbd4 16 34 33
  • 78.16 (n)
rat
(Rattus norvegicus)
Mammalia Mbd4 33
  • 77.92 (n)
oppossum
(Monodelphis domestica)
Mammalia MBD4 34
  • 57 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia MBD4 34
  • 43 (a)
OneToOne
chicken
(Gallus gallus)
Aves MBD4 34
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia MBD4 34
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6790 33
zebrafish
(Danio rerio)
Actinopterygii Dr.16765 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 56 (a)
OneToMany
Cin.8051 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8051 33
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)
Aminode:
Evolutionary constrained regions (ECRs) for MBD4: view image

Paralogs for MBD4 Gene

Paralogs for MBD4 Gene

(1) SIMAP similar genes for MBD4 Gene using alignment to 3 proteins:

  • MBD4_HUMAN
  • D6RBI7_HUMAN
  • E9PEE4_HUMAN
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 Variation AA Info Type
rs148987764 uncertain-significance, Cranioectodermal dysplasia 129,440,121(-) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs267607193 pathogenic, Cranioectodermal dysplasia 1 129,440,351(-) G/C upstream_transcript_variant
rs3138334 likely-benign, Cranioectodermal dysplasia 129,440,125(-) A/G 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs367704478 uncertain-significance, Cranioectodermal dysplasia 129,440,328(-) G/A upstream_transcript_variant
rs2307293 uncertain-significance, not specified 129,431,542(-) C/G 3_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, missense_variant

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)

Additional Variant Information for MBD4 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for MBD4 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
rett syndrome
  • rtt
cranioectodermal dysplasia 1
  • ced1
hyperplastic polyposis syndrome
  • serrated polyposis
angelman syndrome
  • as
autism
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards
Search MBD4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MBD4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 22 58
  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 22 58
  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 44 58
  4. The Glu346Lys polymorphism and frameshift mutations of the Methyl-CpG Binding Domain 4 gene in gastrointestinal cancer. (PMID: 19469655) Song JH … Park WS (Neoplasma 2009) 3 22 44 58
  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 (Amsterdam, Netherlands) 2008) 3 22 44 58

Products for MBD4 Gene

Sources for MBD4 Gene

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