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Guidelines

MIRAGE

methyl-CpG binding domain 4, DNA glycosylase

Summary

Gene Symbol

MBD4

Aliases

MED1

Organism

Homo sapiens (human)

External Links

NCBI Gene

8930

HGNC

6919

PubChem

8930

Alliance of Genome Resources

HGNC:6919

JoGo

MBD4

TogoVar

MBD4

Annotation

Keyword

3D-structure
Alternative splicing
DNA repair
DNA-binding
Disease variant
Hydrolase
Nucleus
Phosphoprotein
Proteomics identification
Reference proteome

Proteins

Displaying 1 entry
UniProt	Protein Name
O95243	Methyl-CpG-binding endonuclease 1 Methyl-CpG-binding protein MBD4 Mismatch-specific DNA N-glycosylase

Annotation information from UniProt.

Gene Ontology (GO)

Displaying entries **1 - 5** of 6 in total

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GO Term	Evidence Code	PMID
DNA repair	TAS
DNA repair	IEA
DNA damage response	IEA
cellular response to DNA damage stimulus	IEA
response to estradiol	IEA

GO Hierarchy

biological process

cellular process [inference]

metabolic process [inference]

phosphorus metabolic process [inference]

phosphate-containing compound metabolic process [inference]

nucleoside phosphate metabolic process [inference]

nucleotide metabolic process [inference]

pyrimidine nucleotide metabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

2'-deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

deoxyribose phosphate catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

organophosphate metabolic process [inference]

nucleoside phosphate metabolic process [inference]

nucleotide metabolic process [inference]

pyrimidine nucleotide metabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

2'-deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

organophosphate catabolic process [inference]

deoxyribose phosphate catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

catabolic process [inference]

nucleobase-containing compound catabolic process [inference]

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

organophosphate catabolic process [inference]

deoxyribose phosphate catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine-containing compound catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

carbohydrate derivative catabolic process [inference]

deoxyribose phosphate catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

macromolecule metabolic process [inference]

macromolecule modification [inference]

DNA modification [inference]

depyrimidination

nucleic acid metabolic process [inference]

DNA metabolic process [inference]

DNA repair

base-excision repair, AP site formation [inference]

depyrimidination

DNA modification [inference]

depyrimidination

primary metabolic process [inference]

nucleobase-containing compound metabolic process [inference]

nucleobase-containing compound catabolic process [inference]

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleobase-containing small molecule metabolic process [inference]

nucleoside phosphate metabolic process [inference]

nucleotide metabolic process [inference]

pyrimidine nucleotide metabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

2'-deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleic acid metabolic process [inference]

DNA metabolic process [inference]

DNA repair

base-excision repair, AP site formation [inference]

depyrimidination

DNA modification [inference]

depyrimidination

small molecule metabolic process [inference]

nucleobase-containing small molecule metabolic process [inference]

nucleoside phosphate metabolic process [inference]

nucleotide metabolic process [inference]

pyrimidine nucleotide metabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

2'-deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

nucleoside phosphate catabolic process [inference]

nucleotide catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine-containing compound metabolic process [inference]

pyrimidine nucleotide metabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

pyrimidine-containing compound catabolic process [inference]

pyrimidine nucleotide catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

carbohydrate derivative metabolic process [inference]

2'-deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide metabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

carbohydrate derivative catabolic process [inference]

deoxyribose phosphate catabolic process [inference]

pyrimidine deoxyribonucleotide catabolic process [inference]

depyrimidination

cellular response to stimulus [inference]

cellular response to stress [inference]

cellular response to DNA damage stimulus

DNA repair

response to stimulus [inference]

response to stress [inference]

cellular response to stress [inference]

cellular response to DNA damage stimulus

DNA repair

response to chemical [inference]

response to lipid [inference]

response to estradiol

response to oxygen-containing compound [inference]

response to estradiol

cellular response to stimulus [inference]

cellular response to stress [inference]

cellular response to DNA damage stimulus

DNA repair

Displaying **all 5** entries
GO Term	Evidence Code	PMID
nucleus	TAS
nucleus	IBA
nucleus	IEA
nucleoplasm	TAS
nuclear speck	IDA

GO Hierarchy

cellular component

cellular anatomical structure [inference]

nucleoplasm

organelle [inference]

membrane-bounded organelle [inference]

intracellular membrane-bounded organelle [inference]

nucleus

membraneless organelle [inference]

intracellular membraneless organelle [inference]

nuclear body [inference]

nuclear ribonucleoprotein granule [inference]

nuclear speck

ribonucleoprotein granule [inference]

nuclear ribonucleoprotein granule [inference]

nuclear speck

intracellular organelle [inference]

intracellular membrane-bounded organelle [inference]

nucleus

intracellular membraneless organelle [inference]

nuclear body [inference]

nuclear ribonucleoprotein granule [inference]

nuclear speck

ribonucleoprotein granule [inference]

nuclear ribonucleoprotein granule [inference]

nuclear speck

supramolecular complex [inference]

ribonucleoprotein granule [inference]

nuclear ribonucleoprotein granule [inference]

nuclear speck

Displaying entries **1 - 5** of 10 in total

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GO Term	Evidence Code	PMID
DNA binding	IBA
DNA binding	IEA
satellite DNA binding	TAS
catalytic activity	IEA
endodeoxyribonuclease activity	TAS

GO Hierarchy

molecular function

catalytic activity

hydrolase activity [inference]

hydrolase activity, acting on glycosyl bonds [inference]

hydrolase activity, hydrolyzing N-glycosyl compounds [inference]

DNA N-glycosylase activity

mismatch base pair DNA N-glycosylase activity [inference]

pyrimidine-specific mismatch base pair DNA N-glycosylase activity

catalytic activity, acting on a nucleic acid [inference]

nuclease activity [inference]

endonuclease activity [inference]

endodeoxyribonuclease activity

DNA nuclease activity [inference]

endodeoxyribonuclease activity

catalytic activity, acting on DNA [inference]

DNA nuclease activity [inference]

endodeoxyribonuclease activity

DNA N-glycosylase activity

mismatch base pair DNA N-glycosylase activity [inference]

pyrimidine-specific mismatch base pair DNA N-glycosylase activity

binding [inference]

nucleic acid binding [inference]

double-stranded DNA binding [inference]

sequence-specific double-stranded DNA binding [inference]

satellite DNA binding

sequence-specific DNA binding [inference]

sequence-specific double-stranded DNA binding [inference]

satellite DNA binding

protein binding

Gene Ontology information from NCBI Gene and UniProt.

OrthoDB (Group)

Group level

Eukaryota

Group Name

methyl-CpG-binding domain protein 4

Functional Category

K: Transcription
L: Replication, recombination and repair
T: Signal transduction mechanisms

Displaying **all 2** entries
Gene Ontology
DNA repair
catalytic activity

Displaying **all 2** entries
InterPro
DNA glycosylase
Methyl-CpG binding protein MeCP2/MBD4

Human Protein Atlas

ENSG00000129071

Tissue with high expression from Human Protein Atlas. Tissues that are highly expressed are highlighted.

Data available from v23.0.proteinatlas.org. Image credit: Human Protein Atlas

Disease

Disease Ontology

Displaying **all 5** entries
DO ID	Disease Name	Source
DOID:0080199	colorectal carcinoma	Alliance of Genome Resources
DOID:1324	lung cancer	Alliance of Genome Resources
DOID:3748	esophagus squamous cell carcinoma	Alliance of Genome Resources
DOID:6039	uveal melanoma	Alliance of Genome Resources
DOID:7148	rheumatoid arthritis	Alliance of Genome Resources

The Human Phenotype Ontology

Displaying entries **1 - 10** of 11 in total

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HPO ID	HPO Term
HP:0000006	Autosomal dominant inheritance
HP:0002858	Meningioma
HP:0003003	Colon cancer
HP:0003581	Adult onset
HP:0003596	Middle age onset
HP:0003621	Juvenile onset
HP:0004808	Acute myeloid leukemia
HP:0005227	Adenomatous colonic polyposis
HP:0007716	Uveal melanoma
HP:0011462	Young adult onset

Displaying **all 2** entries
Disease ID	Disease Name
OMIM:619975	tumor predisposition syndrome 2
OMIM:606660	melanoma, uveal, susceptibility to, 1

PubChem Disease

MedGen Diseases

OMIM Phenotypes

KEGG Diseases

Tumor predisposition syndrome

Gene-Disease-Co-Occurrences-in-Literature (PubChem)

ChIP-Atlas

Target Genes: Predicted target genes bound by given transcription factors. Target Genes
Potential target genes for MBD4
Distance from TSS: ± 10 kb

Displaying entries **1 - 10** of **188** in total

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Gene Symbol	Description	Cellline (score)
XXYLT1	xyloside xylosyltransferase 1	Hep_G2(102)
C1GALT1C1L	C1GALT1 specific chaperone 1 like	Hep_G2(116)
GANAB	glucosidase II alpha subunit	Hep_G2(199)
ACYP2	acylphosphatase 2	Hep_G2(109)
SACM1L	SAC1 like phosphatidylinositide phosphatase	Hep_G2(204)
PIGO	phosphatidylinositol glycan anchor biosynthesis class O	Hep_G2(118)
IL1RAP	interleukin 1 receptor accessory protein	Hep_G2(117)
AADAC	arylacetamide deacetylase	Hep_G2(117)
SRP54	signal recognition particle 54	Hep_G2(266)
GBGT1	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group)	Hep_G2(98)

Colocalization: Predicted partner proteins colocalizing with given transcription factors. Colocalization
Colocalization analysis for MBD4

Displaying **all 4** entries
Gene Symbol	Description	Cellline (score)
MBD4	methyl-CpG binding domain 4, DNA glycosylase	Hep_G2(10)
INSR	insulin receptor	Hep_G2(0)
INO80	INO80 complex ATPase subunit	Hep_G2(0) HuH-7(0)
HDAC2	histone deacetylase 2	Hep_G2(9)

An integrative, comprehensive database to explore public Epigenetic dataset, including ChIP-Seq, DNase-Seq, ATAC-Seq, and Bisulfite-Seq data: ChIP-Atlas covers almost all public data archived in Sequence Read Archive of NCBI, EBI, and DDBJ with over 224,000 experiments.

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Acknowledgements

Supported by JST NBDC Grant Number JPMJND2204

Partly supported by NIH Common Fund Grant #1U01GM125267-01

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Last updated: April 6, 2026