Mbd4 MGI Mouse Gene Detail - MGI:1333850 - methyl-CpG binding domain protein 4

Symbol

Mbd4
Name

methyl-CpG binding domain protein 4
Synonyms

Med1

Feature Type

protein coding gene
IDs

MGI:1333850
NCBI Gene: 17193
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr6:115817658-115830332 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 53.72 cM
Mapping Data

3 experiments

SNPs within 2kb

409 from dbSNP Build 142
Strain Annotations

18
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1333850	protein coding gene	Chr6:115817658-115830361 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0031157	protein coding gene	Chr6:118485098-118497557 (-)
A/J	MGP_AJ_G0031127	protein coding gene	Chr6:113938296-113950970 (-)
AKR/J	MGP_AKRJ_G0031057	protein coding gene	Chr6:116994796-117007250 (-)
BALB/cJ	MGP_BALBcJ_G0031137	protein coding gene	Chr6:113742860-113755534 (-)
C3H/HeJ	MGP_C3HHeJ_G0030571	protein coding gene	Chr6:67293957-67306400 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0031596	protein coding gene	Chr6:121508101-121520712 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028760	protein coding gene	Chr6:110939531-110952952 (-)
CAST/EiJ	MGP_CASTEiJ_G0030244	protein coding gene	Chr6:117368187-117380937 (-)
CBA/J	MGP_CBAJ_G0030823	protein coding gene	Chr6:126276885-126293656 (-)
DBA/2J	MGP_DBA2J_G0030977	protein coding gene	Chr6:112858201-112870701 (-)
FVB/NJ	MGP_FVBNJ_G0030930	protein coding gene	Chr6:112037275-112050117 (-)
LP/J	MGP_LPJ_G0031056	protein coding gene	Chr6:118495416-118507843 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0030965	protein coding gene	Chr6:130444956-130457413 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031624	protein coding gene	Chr6:117017419-117029878 (-)
PWK/PhJ	MGP_PWKPhJ_G0029960	protein coding gene	Chr6:111874270-111886802 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0029788	protein coding gene	Chr6:115734652-115748239 (-)
WSB/EiJ	MGP_WSBEiJ_G0030328	protein coding gene	Chr6:117281059-117293490 (-)

Human Ortholog

MBD4, methyl-CpG binding domain 4, DNA glycosylase

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

MBD4, methyl-CpG binding domain 4, DNA glycosylase
Synonyms

MED1, TPDS2, UVM1
Links

HGNC:6919

NCBI Gene ID: 8930

neXtProt AC: NX_O95243

UniProt: O95243
Chr Location

3q21.3; chr3:129430947-129440179 (-) GRCh38

MGI Vertebrate Homology

Mbd4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: MBD4
Protein SuperFamily

Methyl_CpG_bd_MBD4
Gene Tree

Mbd4

Diseases

5 with human MBD4 associations

				Human Disease	Mouse Models
				colorectal carcinoma IDs colorectal carcinoma DOID:0080199 EFO:1001951 MESH:D015179 NCI:C2955 UMLS_CUI:C0009402
				esophagus squamous cell carcinoma IDs esophagus squamous cell carcinoma DOID:3748 MESH:D000077277 NCI:C4024 UMLS_CUI:C0279626
				lung cancer IDs lung cancer DOID:1324 DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493
				rheumatoid arthritis IDs rheumatoid arthritis DOID:7148 EFO:0000685 ICD10CM:M06.9 ICD9CM:714.0 KEGG:05323 MESH:D001172 NCI:C2884 OMIM:180300 UMLS_CUI:C0003873
				uveal melanoma IDs uveal melanoma DOID:6039 MESH:C536494 NCI:C7712 OMIM:155720 OMIM:606660 OMIM:606661 ORDO:39044 UMLS_CUI:C0220633

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

30 phenotypes from 4 alleles in 6 genetic backgrounds
5 phenotypes from multigenic genotypes
1 images
20 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

10
Endonuclease-mediated

1
Gene trapped

2
Spontaneous

1
Targeted

6
Genomic Mutations

1 involving Mbd4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

32 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele have an increased rate of DNA mutation, specifically at CpGs.

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All GO Annotations

13
GO References

8

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

845
Tissues

129
cDNA Data

35
Literature Summary

9

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase mbd4

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All Sequences

68
RefSeq

21
UniProt

7
CCDS

CCDS39603.1

Ensembl

ENSMUSG00000030322 (Evidence)
NCBI Gene

17193

			Length	Strain/Species	Flank
genomic	ENSMUSG00000030322	Ensembl Gene Model \| MGI Sequence Detail	12675	C57BL/6J	± kb
transcript	ENSMUST00000032469	Ensembl \| MGI Sequence Detail	3614	Not Applicable
polypeptide	ENSMUSP00000032469	Ensembl \| MGI Sequence Detail	554	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000010218 methyl-CpG-binding domain protein 4

(term hierarchy)
PDB

1NGN, 3VXV, 3VXX, 3VYB, 3VYQ, 4EVV, 4EW0, 4EW4
EC

3.2.2.-
InterPro Domains

IPR016177 DNA-binding domain superfamily

IPR011257 DNA glycosylase

IPR003265 HhH-GPD domain

IPR017352 Methyl-CpG-binding domain protein 4

IPR045138 Methyl-CpG binding protein MeCP2/MBD4

IPR001739 Methyl-CpG DNA binding

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All nucleic 40

Genomic 1

cDNA 36

Primer pair 3

Microarray probesets 5

Summaries

All 64

Developmental Gene Expression 9

Gene Ontology 8

Phenotypes 20
Earliest

J:50520 Hendrich B, et al., Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol. 1998 Nov;18(11):6538-47
Latest

J:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Mbd4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr62539	Chr6:115830307-115830350 (-)	3 bp
Tssr62538	Chr6:115830260-115830304 (-)	50 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24