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

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, Jan 2025]
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

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_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Mbd4 is a component of mismatch repair-directed DNA end processing.
Title: MBD4 Facilitates Immunoglobulin Class Switch Recombination.
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.
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.
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.
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.
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.
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)

Endonuclease-mediated (1)
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AF072249 (e-PCR)
- UniSTS:163398

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

Mbd4 (e-PCR), detects polymorphism
- UniSTS:547454

Mbd4 (e-PCR), detects polymorphism
- UniSTS:525695

Mbd4 (e-PCR), detects polymorphism
- UniSTS:143837

PMC137523P1 (e-PCR)
- UniSTS:270832

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

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
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
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

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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)

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

Status: VALIDATED

Source sequence(s)

AC109169

UniProtKB/Swiss-Prot

Q792D2, Q8R3R3, Q9Z2D7
NM_001410107.1 → NP_001397036.1 methyl-CpG-binding domain protein 4 isoform 3

Status: VALIDATED

Source sequence(s)

AC109169

UniProtKB/Swiss-Prot

Q792D2, Q8R3R3, Q9Z2D7
NM_001410108.1 → NP_001397037.1 methyl-CpG-binding domain protein 4 isoform 4

Status: VALIDATED

Source sequence(s)

AC109169

UniProtKB/Swiss-Prot

Q792D2, Q8R3R3, Q9Z2D7
NM_001410109.1 → NP_001397038.1 methyl-CpG-binding domain protein 4 isoform 5

Status: VALIDATED

Source sequence(s)

AC109169

UniProtKB/TrEMBL

A0A0N4SWA0, Q3UG18

Related

ENSMUSP00000145433.2, ENSMUST00000122816.3
NM_001410110.1 → NP_001397039.1 methyl-CpG-binding domain protein 4 isoform 6

Status: VALIDATED

Source sequence(s)

AC109169

UniProtKB/TrEMBL

Q3TU27, Q3UG18

Related

ENSMUSP00000125619.2, ENSMUST00000147282.4
NM_010774.3 → NP_034904.2 methyl-CpG-binding domain protein 4 isoform 1

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

NR_176942.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC109169
NR_176943.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC109169
NR_176944.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC109169
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

NC_000072.7 Reference GRCm39 C57BL/6J

Range

115817658..115830361 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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