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    Mbd4 methyl-CpG binding domain protein 4 [ Mus musculus (house mouse) ]

    Gene ID: 17193, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Mbd4provided by MGI
    Official Full Name
    methyl-CpG binding domain protein 4provided by MGI
    Primary source
    MGI:MGI:1333850
    See related
    Ensembl:ENSMUSG00000030322 AllianceGenome:MGI:1333850
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Med1
    Summary
    Enables DNA binding activity. Acts upstream of or within intrinsic apoptotic signaling pathway in response to DNA damage; mitotic G2 DNA damage checkpoint signaling; and response to radiation. Located in chromatin; cytoplasm; and nucleus. Is expressed in several structures, including central nervous system; lower urogenital tract; reproductive system; retina; and urethra epithelium. Human ortholog(s) of this gene implicated in colorectal carcinoma; esophagus squamous cell carcinoma; lung cancer; and rheumatoid arthritis. Orthologous to human MBD4 (methyl-CpG binding domain 4, DNA glycosylase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in CNS E11.5 (RPKM 4.6), limb E14.5 (RPKM 3.1) and 21 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    6 E3; 6 53.72 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (115817658..115830361, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (115840697..115853400, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E4857 Neighboring gene small nucleolar RNA, H/ACA box 7A Neighboring gene ribosomal protein L32 Neighboring gene EF-hand calcium binding domain 12 Neighboring gene STARR-positive B cell enhancer ABC_E2201 Neighboring gene STARR-positive B cell enhancer ABC_E11332 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:115803828-115803937 Neighboring gene intraflagellar transport 122 Neighboring gene rhodopsin Neighboring gene STARR-positive B cell enhancer mm9_chr6:115895647-115895947 Neighboring gene rhodopsin enhancer region Neighboring gene H1.8 linker histone

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. MBD4 Facilitates Immunoglobulin Class Switch Recombination. Grigera F, et al. Mol Cell Biol, 2017 Jan 15. PMID 27777312, Free PMC Article
    2. The Mbd4 DNA glycosylase protects mice from inflammation-driven colon cancer and tissue injury. Yu AM, et al. Oncotarget, 2016 May 10. PMID 27086921, Free PMC Article
    3. Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Hashimoto H, et al. Nucleic Acids Res, 2012 Sep 1. PMID 22740654, Free PMC Article
    4. MBD4 deficiency does not increase mutation or accelerate tumorigenesis in mice lacking MMR. Sansom OJ, et al. Oncogene, 2004 Jul 22. PMID 15184874
    5. Cutting edge: the G-U mismatch glycosylase methyl-CpG binding domain 4 is dispensable for somatic hypermutation and class switch recombination. Bardwell PD, et al. J Immunol, 2003 Feb 15. PMID 12574322

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Metastasis-associated lung adenocarcinoma transcript 1 induces methyl-CpG-binding domain protein 4 in mice with recurrent spontaneous abortion caused by anti-phospholipid antibody positivity.
      Title: Metastasis-associated lung adenocarcinoma transcript 1 induces methyl-CpG-binding domain protein 4 in mice with recurrent spontaneous abortion caused by anti-phospholipid antibody positivity.
    2. Expression of mBD4, mBD3 and CRAMP during type II collagen-induced arthritis/CIA and their association with inflammation and bone-remodeling markers.
      Title: Expression of mBD4, mBD3 and CRAMP during type II collagen-induced arthritis/CIA and their association with inflammation and bone-remodeling markers.
    3. Mbd4-/- mice displayed more severe symptoms, decreased survival, and a greater tumor burden than wild-type (WT) controls.
      Title: The Mbd4 DNA glycosylase protects mice from inflammation-driven colon cancer and tissue injury.
    4. Mbd4 is a component of mismatch repair-directed DNA end processing.
      Title: MBD4 Facilitates Immunoglobulin Class Switch Recombination.
    5. A variant Mbd4 transcript spanning exons 1,6-8 is expressed in Mbd4 deficient B cells.
      Title: Complex relationship between mismatch repair proteins and MBD4 during immunoglobulin class switch recombination.
    6. the crystal structure of MBD4 bound to 5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able to recognize a wide range of 5-methylcytosine modifications
      Title: Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.
    7. Studies on a complex A mutant mouse, defective for the Ift122 gene, is reported.
      Title: Defective ciliogenesis, embryonic lethality and severe impairment of the Sonic Hedgehog pathway caused by inactivation of the mouse complex A intraflagellar transport gene Ift122/Wdr10, partially overlapping with the DNA repair gene Med1/Mbd4.
    8. Data report the characterization of interactions between Dnmt3b and both thymine-DNA glycosylase (Tdg) and methyl-CpG binding domain protein 4.
      Title: Characterization of Dnmt3b:thymine-DNA glycosylase interaction and stimulation of thymine glycosylase-mediated repair by DNA methyltransferase(s) and RNA.
    9. structure and activity of the mismatch-specific thymine glycosylase domain of MBD4
      Title: Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
    10. studies indicate that, although inactivation of Mbd4 does not by itself cause cancer predisposition in mice, it can alter the mutation spectrum in cancer cells and modify the cancer predisposition phenotype
      Title: Mbd4 inactivation increases Cright-arrowT transition mutations and promotes gastrointestinal tumor formation.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (4)  1 citation
    • Endonuclease-mediated (1) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pyrimidine-specific mismatch base pair DNA N-glycosylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within mitotic G2 DNA damage checkpoint signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to radiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    methyl-CpG-binding domain protein 4
    Names
    methyl-CpG-binding protein MBD4
    mismatch-specific DNA N-glycosylase

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001410106.1 → NP_001397035.1  methyl-CpG-binding domain protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC109169

    2. NM_001410107.1 → NP_001397036.1  methyl-CpG-binding domain protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC109169

    3. NM_001410108.1 → NP_001397037.1  methyl-CpG-binding domain protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC109169

    4. NM_001410109.1 → NP_001397038.1  methyl-CpG-binding domain protein 4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC109169
      UniProtKB/TrEMBL
      A0A0N4SWA0
      Related
      ENSMUSP00000145433.2, ENSMUST00000122816.3

    5. NM_001410110.1 → NP_001397039.1  methyl-CpG-binding domain protein 4 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC109169
      UniProtKB/TrEMBL
      Q3TU27
      Related
      ENSMUSP00000125619.2, ENSMUST00000147282.4

    6. NM_010774.3 → NP_034904.2  methyl-CpG-binding domain protein 4 isoform 1

      See identical proteins and their annotated locations for NP_034904.2

      Status: VALIDATED

      Source sequence(s)
      AC109169
      Consensus CDS
      CCDS39603.1
      UniProtKB/Swiss-Prot
      Q792D2, Q8R3R3, Q9Z2D7
      UniProtKB/TrEMBL
      A0A0R4J0A8
      Related
      ENSMUSP00000032469.7, ENSMUST00000032469.13
      Conserved Domains (2) summary
      smart00391
      Location:66 → 132
      MBD; Methyl-CpG binding domain
      cl23768
      Location:424 → 510
      ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

    RNA

    1. NR_176942.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC109169

    2. NR_176943.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC109169

    3. NR_176944.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC109169

    4. NR_176945.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC109169

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      115817658..115830361 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006505683.5 → XP_006505746.1  methyl-CpG-binding domain protein 4 isoform X3

      See identical proteins and their annotated locations for XP_006505746.1

      UniProtKB/TrEMBL
      Q3UGS3
      Conserved Domains (1) summary
      cl23768
      Location:2 → 48
      ENDO3c; endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases

    RNA

    1. XR_004942916.1 RNA Sequence

    2. XR_001785104.3 RNA Sequence

    3. XR_004942917.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Z2D7.1 GenPept UniProtKB/Swiss-Prot:Q9Z2D7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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