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Mbd3 methyl-CpG binding domain protein 3 [ Mus musculus (house mouse) ]

Gene ID: 17192, updated on 8-Feb-2024

Summary

Official Symbol
Mbd3provided by MGI
Official Full Name
methyl-CpG binding domain protein 3provided by MGI
Primary source
MGI:MGI:1333812
See related
Ensembl:ENSMUSG00000035478 AllianceGenome:MGI:1333812
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
This gene encodes a member of the MBD family of nuclear proteins that contain a methyl-CpG binding domain (MBD). The encoded protein is a component of the nucleosome remodeling and histone deacetylation (NuRD) complex. Deletion of this gene causes embryonic lethality in mice. Embryonic stem cells lacking the encoded protein are severely compromised in their ability to differentiate and fail to commit to developmental lineages in the absence of leukemia inhibitory factor. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 83.1), ovary adult (RPKM 79.9) and 28 other tissues See more
Orthologs
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Genomic context

See Mbd3 in Genome Data Viewer
Location:
10 C1; 10 39.72 cM
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (80228373..80235365, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (80392539..80399531, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene polo like kinase 5 Neighboring gene mex3 RNA binding family member D Neighboring gene predicted gene, 30823 Neighboring gene RIKEN cDNA 3300002P09 gene Neighboring gene STARR-positive B cell enhancer ABC_E5156 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene transcription factor 3 Neighboring gene STARR-positive B cell enhancer ABC_E9795 Neighboring gene STARR-positive B cell enhancer ABC_E6881 Neighboring gene STARR-positive B cell enhancer ABC_E367

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)

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 IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
 
enables methyl-CpG binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables methyl-CpG binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
part_of NuRD complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of NuRD complex ISO
Inferred from Sequence Orthology
more info
 
part_of NuRD complex NAS
Non-traceable Author Statement
more info
PubMed 
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
part_of heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
NOT located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
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 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
methyl-CpG-binding domain protein 3
Names
methyl-CpG-binding protein MBD3

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_001306143.1NP_001293072.1  methyl-CpG-binding domain protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001293072.1

    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 has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC152062, BP770230, BQ042794, CK625083
    Consensus CDS
    CCDS78860.1
    UniProtKB/TrEMBL
    D3YTR5
    Related
    ENSMUSP00000100986.2, ENSMUST00000105349.8
    Conserved Domains (3) summary
    pfam14048
    Location:121211
    MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
    pfam16564
    Location:51116
    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 ...
  2. NM_013595.3NP_038623.1  methyl-CpG-binding domain protein 3 isoform 1

    See identical proteins and their annotated locations for NP_038623.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC152062, BP770230, BQ042794, CK625083, CX208033
    Consensus CDS
    CCDS24020.1
    UniProtKB/Swiss-Prot
    Q792D3, Q8CFJ1, Q9Z2D8
    UniProtKB/TrEMBL
    D3YTR5
    Related
    ENSMUSP00000089948.4, ENSMUST00000092295.10
    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:83148
    MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

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_000076.7 Reference GRCm39 C57BL/6J

    Range
    80228373..80235365 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)