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MECP2 methyl-CpG binding protein 2 [ Homo sapiens (human) ]

Gene ID: 4204, updated on 8-Jul-2018
Official Symbol
MECP2provided by HGNC
Official Full Name
methyl-CpG binding protein 2provided by HGNC
Primary source
HGNC:HGNC:6990
See related
Ensembl:ENSG00000169057 MIM:300005; Vega:OTTHUMG00000024229
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RS; RTS; RTT; PPMX; MRX16; MRX79; MRXSL; AUTSX3; MRXS13
Summary
DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
Expression
Ubiquitous expression in ovary (RPKM 10.4), brain (RPKM 8.2) and 25 other tissues See more
Orthologs
See MECP2 in Genome Data Viewer
Location:
Xq28
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (154021800..154097731, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153287025..153363188, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NFE2L2 motif-containing MPRA enhancer 190/191 Neighboring gene interleukin 1 receptor associated kinase 1 Neighboring gene microRNA 718 Neighboring gene opsin locus control region Neighboring gene opsin 1, long wave sensitive Neighboring gene testis expressed 28 pseudogene 2

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-05)

ClinGen Genome Curation Page
Triplosensitivity

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-05)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Common variants on Xq28 conferring risk of schizophrenia in Han Chinese.
NHGRI GWA Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Nef nef MECP2 mRNA is selectively retained in HIV-1 Nef-expressing cellular exosomes, and eight miRNAs (miR-19a, miR-29b, miR-34a*, miR-146b, miR-181a, miR181c, miR-195, and let-7c) which target MECP2 mRNA are selectively secreted in exosomes from these cells PubMed

Go to the HIV-1, Human Interaction Database

  • Cytosine methylation, organism-specific biosystem (from WikiPathways)
    Cytosine methylation, organism-specific biosystemDNA, namely cytosine, methylation is the key event in epigentics. The degree of methylation influences gene expression and methylation disorders are known to be major causes of some diseases like Ret...
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Lung fibrosis, organism-specific biosystem (from WikiPathways)
    Lung fibrosis, organism-specific biosystemLung fibrosis pathway linked to events (molecular initiating event, key events and associative events) in a putative Adverse Outcome Pathway for lung fibrosis.
  • MECP2 and Associated Rett Syndrome, organism-specific biosystem (from WikiPathways)
    MECP2 and Associated Rett Syndrome, organism-specific biosystemMecp2 is in many mammals an important regulator of neuronal function and development. It affects all cell types, especially neurons but also astrocytes, oligodendrocytes, and glial cells. Mecp2 plays...
  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • DKFZp686A24160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding TAS
Traceable Author Statement
more info
PubMed 
RNA binding HDA PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded methylated DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded methylated DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
 
methyl-CpG binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
siRNA binding IEA
Inferred from Electronic Annotation
more info
 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
behavioral fear response IEA
Inferred from Electronic Annotation
more info
 
cardiolipin metabolic process IEA
Inferred from Electronic Annotation
more info
 
catecholamine secretion IEA
Inferred from Electronic Annotation
more info
 
cellular biogenic amine metabolic process IEA
Inferred from Electronic Annotation
more info
 
cerebellum development IEA
Inferred from Electronic Annotation
more info
 
chromatin silencing IEA
Inferred from Electronic Annotation
more info
 
dendrite development IEA
Inferred from Electronic Annotation
more info
 
excitatory postsynaptic potential IEA
Inferred from Electronic Annotation
more info
 
glucocorticoid metabolic process IEA
Inferred from Electronic Annotation
more info
 
glutamine metabolic process IEA
Inferred from Electronic Annotation
more info
 
histone acetylation IEA
Inferred from Electronic Annotation
more info
 
histone methylation IEA
Inferred from Electronic Annotation
more info
 
inositol metabolic process IEA
Inferred from Electronic Annotation
more info
 
locomotory behavior IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
long-term memory IEA
Inferred from Electronic Annotation
more info
 
long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
 
mitochondrial electron transport, ubiquinol to cytochrome c IEA
Inferred from Electronic Annotation
more info
 
mitotic spindle organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of blood vessel endothelial cell migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of histone acetylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of histone methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
neurological system process involved in regulation of systemic arterial blood pressure IEA
Inferred from Electronic Annotation
more info
 
neuron maturation IEA
Inferred from Electronic Annotation
more info
 
pathogenesis IEA
Inferred from Electronic Annotation
more info
 
phosphatidylcholine metabolic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of microtubule nucleation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
proprioception IEA
Inferred from Electronic Annotation
more info
 
protein localization IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
 
regulation of respiratory gaseous exchange by neurological system process IEA
Inferred from Electronic Annotation
more info
 
respiratory gaseous exchange IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to radiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sensory perception of pain IEA
Inferred from Electronic Annotation
more info
 
social behavior IEA
Inferred from Electronic Annotation
more info
 
startle response IEA
Inferred from Electronic Annotation
more info
 
synapse assembly IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
ventricular system development IEA
Inferred from Electronic Annotation
more info
 
visual learning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with centrosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space HDA PubMed 
colocalizes_with gamma-tubulin complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
postsynapse IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
methyl-CpG-binding protein 2
Names
meCp-2 protein
testis tissue sperm-binding protein Li 41a

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.

Genomic

  1. NG_007107.2 RefSeqGene

    Range
    44391..120315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001110792.1NP_001104262.1  methyl-CpG-binding protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001104262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as MECP2B, lacks exon 2. Translation is reported to initiate in the first exon resulting in a protein isoform (2) with a distinct N-terminus. This transcript is reported to be abundant in the central nervous system (PMID: 15034579, 17171659).
    Source sequence(s)
    AB209464, BC011612, BX538060
    Consensus CDS
    CCDS48193.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    A0A140VKC4, Q59FJ6
    Related
    ENSP00000395535.2, OTTHUMP00000064436, ENST00000453960.6, OTTHUMT00000061145
    Conserved Domains (1) summary
    smart00391
    Location:104181
    MBD; Methyl-CpG binding domain
  2. NM_001316337.1NP_001303266.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes exon 2 and an additional exon, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AB209464, AF030876, BC011612, BI767019
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    Q59FJ6
    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  3. NM_004992.3NP_004983.1  methyl-CpG-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_004983.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as MECP2A, includes exon 2. Translation is reported to initiate in exon 2 resulting in a protein isoform (1) with a distinct N-terminus.
    Source sequence(s)
    AB209464, AC244097, AF158180
    Consensus CDS
    CCDS14741.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    D3YJ43, Q59FJ6
    Related
    ENSP00000301948.6, OTTHUMP00000026021, ENST00000303391.10, OTTHUMT00000061144
    Conserved Domains (1) summary
    smart00391
    Location:92169
    MBD; Methyl-CpG binding domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    154021800..154097731 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452383.1XP_024308151.1  methyl-CpG-binding protein 2 isoform X1

    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  2. XM_024452384.1XP_024308152.1  methyl-CpG-binding protein 2 isoform X1

    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  3. XM_011531166.2XP_011529468.1  methyl-CpG-binding protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011529468.1

    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  4. XM_006724819.3XP_006724882.1  methyl-CpG-binding protein 2 isoform X2

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