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    MBD3 methyl-CpG binding domain protein 3 [ Homo sapiens (human) ]

    Gene ID: 53615, updated on 5-May-2024

    Summary

    Official Symbol
    MBD3provided by HGNC
    Official Full Name
    methyl-CpG binding domain protein 3provided by HGNC
    Primary source
    HGNC:HGNC:6918
    See related
    Ensembl:ENSG00000071655 MIM:603573; AllianceGenome:HGNC:6918
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in placenta (RPKM 23.4), fat (RPKM 18.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    19p13.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1573596..1592865, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1544415..1563688, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1573595..1592864, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 1835 Neighboring gene mex-3 RNA binding family member D Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9729 Neighboring gene RNA, 7SL, cytoplasmic 477, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1584307-1584918 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1584919-1585529 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1590888-1591877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9734 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1606417-1607038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13618 Neighboring gene RNA, U6 small nuclear 1223, pseudogene Neighboring gene transcription factor 3

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ35189, DKFZp762G113

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables methyl-CpG binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables methyl-CpG binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to nucleosomal DNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of NuRD complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of NuRD complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of chromatin HDA PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    part_of heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    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 
    part_of protein-containing complex HDA PubMed 

    General protein information

    Preferred Names
    methyl-CpG-binding domain protein 3

    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.

    Genomic

    1. NG_029897.3 RefSeqGene

      Range
      5000..24269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001281453.2NP_001268382.1  methyl-CpG-binding domain protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001268382.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC005943
      Consensus CDS
      CCDS12072.1
      UniProtKB/Swiss-Prot
      A8K4B7, D6W5Z2, O95983, Q6PIL9, Q6PJZ9, Q86XF4
      Related
      ENSP00000412302.2, ENST00000434436.8
      Conserved Domains (3) summary
      cd01396
      Location:579
      MeCP2_MBD; MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding ...
      pfam14048
      Location:153243
      MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
      pfam16564
      Location:82148
      MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
    2. NM_001281454.2NP_001268383.1  methyl-CpG-binding domain protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001268383.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
      Source sequence(s)
      AC005943
      Consensus CDS
      CCDS62481.1
      UniProtKB/TrEMBL
      B3KMA8
      Related
      ENSP00000156825.2, ENST00000156825.5
      Conserved Domains (3) summary
      pfam14048
      Location:121211
      MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
      pfam16564
      Location:50116
      MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
      cl00110
      Location:547
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      1573596..1592865 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438939.1XP_047294895.1  methyl-CpG-binding domain protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K4B7, D6W5Z2, O95983, Q6PIL9, Q6PJZ9, Q86XF4
      Related
      ENSP00000464718.1, ENST00000590550.6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      1544415..1563688 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321223.1XP_054177198.1  methyl-CpG-binding domain protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K4B7, D6W5Z2, O95983, Q6PIL9, Q6PJZ9, Q86XF4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_003926.5: Suppressed sequence

      Description
      NM_003926.5: This RefSeq was permanently suppressed because currently there is support for the protein but not for the transcript.