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

    Gene ID: 17193, updated on 27-Nov-2024

    Summary

    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; rheumatoid arthritis; and uveal melanoma. Orthologous to human MBD4 (methyl-CpG binding domain 4, DNA glycosylase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in CNS E11.5 (RPKM 4.6), limb E14.5 (RPKM 3.1) and 21 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Mbd4 in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 pyrimidine-specific mismatch base pair DNA N-glycosylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in 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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001410106.1NP_001397035.1  methyl-CpG-binding domain protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC109169
    2. NM_001410107.1NP_001397036.1  methyl-CpG-binding domain protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC109169
    3. NM_001410108.1NP_001397037.1  methyl-CpG-binding domain protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC109169
    4. NM_001410109.1NP_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_001410110.1NP_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_010774.3NP_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:66132
      MBD; Methyl-CpG binding domain
      cl23768
      Location:424510
      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_006505683.5XP_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:248
      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