Mecp2 methyl CpG binding protein 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Mecp2provided by MGI
Official Full Name: methyl CpG binding protein 2provided by MGI
Primary source: MGI:MGI:99918
See related: Ensembl:ENSMUSG00000031393 AllianceGenome:MGI:99918
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: Mbd5; WBP10; 1500041B07Rik; D630021H01Rik
Summary: Enables several functions, including nucleic acid binding activity; promoter-specific chromatin binding activity; and transcription corepressor activity. Involved in several processes, including negative regulation of smooth muscle cell differentiation; negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation; and positive regulation of histone H3-K9 trimethylation. Acts upstream of or within several processes, including glycerolipid metabolic process; nervous system development; and regulation of gene expression. Located in cytosol; heterochromatin; and nucleus. Is expressed in several structures, including alimentary system; early conceptus; nervous system; paraxial mesenchyme; and sensory organ. Used to study Rett syndrome. Human ortholog(s) of this gene implicated in Rett syndrome; X-linked intellectual disability-psychosis-macroorchidism syndrome; autistic disorder; severe congenital encephalopathy due to MECP2 mutation; and syndromic X-linked intellectual disability Lubs type. Orthologous to human MECP2 (methyl-CpG binding protein 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in whole brain E14.5 (RPKM 8.6), CNS E18 (RPKM 7.6) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: X A7.3; X 37.63 cM

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (73070198..73129296, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (74026592..74085690, complement)

Chromosome X - NC_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Autoimmune and neuropsychiatric phenotypes in a Mecp2 transgenic mouse model on C57BL/6 background.
Title: Autoimmune and neuropsychiatric phenotypes in a Mecp2 transgenic mouse model on C57BL/6 background.
Selective Deletion of Methyl CpG Binding Protein 2 from Parvalbumin Interneurons in the Auditory Cortex Delays the Onset of Maternal Retrieval in Mice.
Title: Selective Deletion of Methyl CpG Binding Protein 2 from Parvalbumin Interneurons in the Auditory Cortex Delays the Onset of Maternal Retrieval in Mice.
RIPK1 activation in Mecp2-deficient microglia promotes inflammation and glutamate release in RTT.
Title: RIPK1 activation in Mecp2-deficient microglia promotes inflammation and glutamate release in RTT.
POMC-specific knockdown of MeCP2 leads to adverse phenotypes in mice chronically exposed to high fat diet.
Title: POMC-specific knockdown of MeCP2 leads to adverse phenotypes in mice chronically exposed to high fat diet.
Tug-of-Peace: Visual Rivalry and Atypical Visual Motion Processing in MECP2 Duplication Syndrome of Autism.
Title: Tug-of-Peace: Visual Rivalry and Atypical Visual Motion Processing in MECP2 Duplication Syndrome of Autism.
Gut microbiome and metabolic profiles of mouse model for MeCP2 duplication syndrome.
Title: Gut microbiome and metabolic profiles of mouse model for MeCP2 duplication syndrome.
MeCP2 represses the activity of topoisomerase IIbeta in long neuronal genes.
Title: MeCP2 represses the activity of topoisomerase IIβ in long neuronal genes.
Systemic proteome phenotypes reveal defective metabolic flexibility in Mecp2 mutants.
Title: Systemic proteome phenotypes reveal defective metabolic flexibility in Mecp2 mutants.
Neuronal MeCP2 in the dentate gyrus regulates mossy fiber sprouting of mice with temporal lobe epilepsy.
Title: Neuronal MeCP2 in the dentate gyrus regulates mossy fiber sprouting of mice with temporal lobe epilepsy.
Spinal astrocytic MeCP2 regulates Kir4.1 for the maintenance of chronic hyperalgesia in neuropathic pain.
Title: Spinal astrocytic MeCP2 regulates Kir4.1 for the maintenance of chronic hyperalgesia in neuropathic pain.

Submit: New GeneRIF Correction See all GeneRIFs (401)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (44) 1 citation
Endonuclease-mediated (18) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BB130002 (e-PCR)
- UniSTS:186172

Mecp2 (e-PCR), detects polymorphism
- UniSTS:472894

Mecp2 (e-PCR), detects polymorphism
- UniSTS:472895

Mecp2 (e-PCR), detects polymorphism
- UniSTS:472896

Mecp2 (e-PCR), detects polymorphism
- UniSTS:472897

ECD14555 (e-PCR)
- UniSTS:295575

REN88559 (e-PCR)
- UniSTS:413357

Mecp2 (e-PCR), detects polymorphism
- UniSTS:507063

REN88847 (e-PCR)
- UniSTS:413645

REN88597 (e-PCR)
- UniSTS:413395

REN88598 (e-PCR)
- UniSTS:413396

NoName (e-PCR)
- UniSTS:238043

Mecp2 (e-PCR), detects polymorphism
- UniSTS:143851

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables double-stranded methylated DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded methylated DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded methylated DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded methylated DNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables four-way junction DNA binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables histone reader activity	IDA Inferred from Direct Assay more info	PubMed
enables histone reader activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpG binding	IBA Inferred from Biological aspect of Ancestor more info
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables molecular condensate scaffold activity	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables siRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables unmethylated CpG binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within adult locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in associative learning	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within behavioral fear response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within biogenic amine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiolipin metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of catecholamine secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to isoquinoline alkaloid	ISO Inferred from Sequence Orthology more info
involved_in cellular response to potassium ion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellum development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chemical synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dendrite development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryo development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epigenetic regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epigenetic regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within excitatory postsynaptic potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within genomic imprinting	ISO Inferred from Sequence Orthology more info
acts_upstream_of glial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glucocorticoid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glutamine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inositol metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within learning	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within long-term memory	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within long-term synaptic potentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within memory	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organismal response to stress	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of astrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendrite extension	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendritic spine development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of locomotion involved in locomotory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of primary miRNA processing	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of respiratory gaseous exchange	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of smooth muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system process involved in regulation of systemic arterial blood pressure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromuscular process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromuscular process controlling posture	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within phosphatidylcholine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of anterograde dense core granule transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of branching morphogenesis of a nerve	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendrite extension	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendritic spine development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of glial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of microtubule nucleation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of retrograde dense core granule transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic plasticity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within proprioception	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of action potential firing threshold	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of respiratory gaseous exchange by nervous system process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of synaptic plasticity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within respiratory gaseous exchange by respiratory system	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to cocaine	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to hypoxia	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to other organism	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within social behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in social behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within startle response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of trans-synaptic signaling by BDNF	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ventricular system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within visual learning	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in centrosome	ISO Inferred from Sequence Orthology more info
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of heterochromatin	IDA Inferred from Direct Assay more info	PubMed
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: methyl-CpG-binding protein 2

Names: meCp-2 protein

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_001081979.2 → NP_001075448.1 methyl-CpG-binding protein 2 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1, also known as alpha) represents the shorter transcript and encodes the longer isoform (1).

Source sequence(s)

AK158664, AL672002, BU700810

Consensus CDS

CCDS41016.1

UniProtKB/Swiss-Prot

Q9Z2D6

Related

ENSMUSP00000033770.7, ENSMUST00000033770.13

Conserved Domains (1) summary

smart00391
Location:109 → 186

MBD; Methyl-CpG binding domain
NM_010788.4 → NP_034918.1 methyl-CpG-binding protein 2 isoform 2

See identical proteins and their annotated locations for NP_034918.1

Status: VALIDATED

Description

Transcript Variant: This variant (2, also known as beta) has an additional exon in the 5' region, which results in the use of an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AL672002, BU700810

Consensus CDS

CCDS41017.1

UniProtKB/Swiss-Prot

B1AUZ2, B1AUZ3, Q3TYG1, Q9Z2D6

Related

ENSMUSP00000098314.4, ENSMUST00000100750.10

Conserved Domains (1) summary

smart00391
Location:92 → 169

MBD; Methyl-CpG binding domain

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_000086.8 Reference GRCm39 C57BL/6J

Range

73070198..73129296 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030251240.1 → XP_030107100.1 methyl-CpG-binding protein 2 isoform X1

UniProtKB/Swiss-Prot

B1AUZ2, B1AUZ3, Q3TYG1, Q9Z2D6

Conserved Domains (1) summary

smart00391
Location:92 → 169

MBD; Methyl-CpG binding domain