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    MBD2 methyl-CpG binding domain protein 2 [ Homo sapiens (human) ]

    Gene ID: 8932, updated on 10-Dec-2024

    Summary

    Official Symbol
    MBD2provided by HGNC
    Official Full Name
    methyl-CpG binding domain protein 2provided by HGNC
    Primary source
    HGNC:HGNC:6917
    See related
    Ensembl:ENSG00000134046 MIM:603547; AllianceGenome:HGNC:6917
    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
    Also known as
    DMTase; NY-CO-41
    Summary
    DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. The protein encoded by this gene may function as a mediator of the biological consequences of the methylation signal. It is also reported that the this protein functions as a demethylase to activate transcription, as DNA methylation causes gene silencing. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 19.7), lymph node (RPKM 18.4) and 25 other tissues See more
    Orthologs
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    Genomic context

    See MBD2 in Genome Data Viewer
    Location:
    18q21.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (54151606..54224669, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (54354681..54427744, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (51677976..51751039, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904304 Neighboring gene long intergenic non-protein coding RNA 1919 Neighboring gene long intergenic non-protein coding RNA 1917 Neighboring gene ribosomal protein L29 pseudogene 32 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:51309208-51310407 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:51377120-51377889 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48020 Neighboring gene NANOG hESC enhancer GRCh37_chr18:51595986-51596496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13338 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:51650065-51650829 Neighboring gene Sharpr-MPRA regulatory region 14779 Neighboring gene NANOG hESC enhancer GRCh37_chr18:51653946-51654503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13340 Neighboring gene MPRA-validated peak3156 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:51751880-51752422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:51752423-51752963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13342 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:51772851-51773736 Neighboring gene uncharacterized LOC124904306 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:51773737-51774623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9471 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:51779086-51779588 Neighboring gene uncharacterized LOC124904307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13345 Neighboring gene small nucleolar RNA, H/ACA box 37 Neighboring gene DNA polymerase iota

    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?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (48 hits/1294 screens)

    EBI GWAS Catalog

    Description
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Methyl-CpG-binding proteins MBD2 and p66alpha are identified to interact with HIV-1 Tat in Jurkat cell PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    General gene information

    Clone Names

    • DKFZp586O0821

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C2H2 zinc finger domain binding PubMed 
    enables identical protein binding  
    enables mRNA binding  
    enables methyl-CpG binding  
    enables methyl-CpG binding PubMed 
    enables methyl-CpG binding PubMed 
    enables molecular adaptor activity PubMed 
    contributes_to nucleosomal DNA binding PubMed 
    enables protein binding PubMed 
    enables protein domain specific binding PubMed 
    enables satellite DNA binding PubMed 
    enables siRNA binding  
    Process Evidence Code Pubs
    involved_in DNA methylation-dependent constitutive heterochromatin formation  
    involved_in DNA methylation-dependent constitutive heterochromatin formation PubMed 
    involved_in Wnt signaling pathway  
    involved_in cellular response to organic cyclic compound  
    involved_in chromatin remodeling PubMed 
    involved_in chromatin remodeling PubMed 
    involved_in embryonic organ development  
    involved_in maternal behavior  
    involved_in negative regulation of DNA-templated transcription PubMed 
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of Wnt signaling pathway  
    involved_in protein-containing complex assembly  
    involved_in regulation of cell population proliferation  
    involved_in response to estradiol  
    involved_in response to mechanical stimulus  
    involved_in response to nutrient levels  
    involved_in ventricular cardiac muscle tissue development  
    Component Evidence Code Pubs
    part_of NuRD complex PubMed 
    part_of NuRD complex PubMed 
    located_in chromatin PubMed 
    located_in chromatin PubMed 
    located_in cytosol  
    located_in heterochromatin  
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in nucleus PubMed 
    part_of protein-containing complex PubMed 

    General protein information

    Preferred Names
    methyl-CpG-binding domain protein 2
    Names
    demethylase

    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.

    Genomic

    1. NG_029550.1 RefSeqGene

      Range
      5120..78183
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003927.5 → NP_003918.1  methyl-CpG-binding domain protein 2 isoform 1

      See identical proteins and their annotated locations for NP_003918.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC090666, AF072242, AW151547
      Consensus CDS
      CCDS11953.1
      UniProtKB/Swiss-Prot
      O95242, Q9UBB5, Q9UIS8
      Related
      ENSP00000256429.3, ENST00000256429.8
      Conserved Domains (3) summary
      cd01396
      Location:151 → 214
      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:297 → 387
      MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
      pfam16564
      Location:226 → 292
      MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
    2. NM_015832.6 → NP_056647.1  methyl-CpG-binding domain protein 2 testis-specific isoform

      See identical proteins and their annotated locations for NP_056647.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate exon in the 3' coding region, compared to variant 1, resulting in a shorter protein (testis-specific) that has a shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC093462, AF072242, AF072246, AW274866
      Consensus CDS
      CCDS45871.1
      Related
      ENSP00000464554.1, ENST00000583046.1
      Conserved Domains (1) summary
      cd01396
      Location:151 → 214
      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 ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      54151606..54224669 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      54354681..54427744 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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