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

Gene ID: 4204, updated on 23-Jun-2022

Summary

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; AllianceGenome:HGNC:6990
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
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Genomic context

See MECP2 in Genome Data Viewer
Location:
Xq28
Exon count:
12
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154021573..154097717, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152295254..152371375, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153287024..153363174, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes 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 TEX28 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-02-22)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-22)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686A24160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding HDA PubMed 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables double-stranded methylated DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables double-stranded methylated DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables mRNA binding IEA
Inferred from Electronic Annotation
more info
 
enables methyl-CpG binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables promoter-specific chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enables protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables siRNA binding IEA
Inferred from Electronic Annotation
more info
 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in behavioral fear response IEA
Inferred from Electronic Annotation
more info
 
involved_in cardiolipin metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in catecholamine secretion IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular biogenic amine metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in cerebellum development IEA
Inferred from Electronic Annotation
more info
 
involved_in dendrite development IEA
Inferred from Electronic Annotation
more info
 
involved_in excitatory postsynaptic potential IEA
Inferred from Electronic Annotation
more info
 
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in glial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in glucocorticoid metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in glutamine metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in heterochromatin assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in histone acetylation IEA
Inferred from Electronic Annotation
more info
 
involved_in histone methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in inositol metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in long-term memory IEA
Inferred from Electronic Annotation
more info
 
involved_in long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in mitotic spindle organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of blood vessel endothelial cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in nervous system process involved in regulation of systemic arterial blood pressure IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron maturation IEA
Inferred from Electronic Annotation
more info
 
involved_in phosphatidylcholine metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of glial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of microtubule nucleation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
involved_in proprioception IEA
Inferred from Electronic Annotation
more info
 
involved_in protein localization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of gene expression by genomic imprinting IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of respiratory gaseous exchange by nervous system process IEA
Inferred from Electronic Annotation
more info
 
involved_in respiratory gaseous exchange by respiratory system IEA
Inferred from Electronic Annotation
more info
 
involved_in response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
involved_in response to other organism IEA
Inferred from Electronic Annotation
more info
 
involved_in sensory perception of pain IEA
Inferred from Electronic Annotation
more info
 
involved_in social behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in startle response IEA
Inferred from Electronic Annotation
more info
 
involved_in synapse assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in trans-synaptic signaling by BDNF IEA
Inferred from Electronic Annotation
more info
 
involved_in ventricular system development IEA
Inferred from Electronic Annotation
more info
 
involved_in visual learning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in centrosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space HDA PubMed 
is_active_in heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
methyl-CpG-binding protein 2
Names
meCp-2 protein

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_007107.3 RefSeqGene

    Range
    44387..120531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_764

mRNA and Protein(s)

  1. NM_001110792.2NP_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)
    AF030876, BC011612, BX538060, U52112
    Consensus CDS
    CCDS48193.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    A0A140VKC4, Q59FJ6
    Related
    ENSP00000395535.2, ENST00000453960.7
    Conserved Domains (1) summary
    smart00391
    Location:104181
    MBD; Methyl-CpG binding domain
  2. NM_001316337.2NP_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. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AB209464, AF030876, BC011612, BI767019, U52112
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    Q59FJ6
    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  3. NM_001369391.2NP_001356320.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes exon 2 and some additional exons, 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. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  4. NM_001369392.2NP_001356321.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) 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. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  5. NM_001369393.2NP_001356322.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks exon 2 and contains 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. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  6. NM_001369394.2NP_001356323.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  7. NM_001386137.1NP_001373066.1  methyl-CpG-binding protein 2 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC244097, AF030876, U52112
  8. NM_001386138.1NP_001373067.1  methyl-CpG-binding protein 2 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC244097, AF030876, U52112
  9. NM_001386139.1NP_001373068.1  methyl-CpG-binding protein 2 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC244097, AF030876, U52112
  10. NM_004992.4NP_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)
    AC244097, AF030876, U52112
    Consensus CDS
    CCDS14741.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    D3YJ43, Q59FJ6
    Related
    ENSP00000301948.6, ENST00000303391.11
    Conserved Domains (1) summary
    smart00391
    Location:92169
    MBD; Methyl-CpG binding domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154021573..154097717 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442116.1XP_047298072.1  methyl-CpG-binding protein 2 isoform X1

  2. XM_047442115.1XP_047298071.1  methyl-CpG-binding protein 2 isoform X1

  3. XM_047442120.1XP_047298076.1  methyl-CpG-binding protein 2 isoform X2

  4. XM_047442119.1XP_047298075.1  methyl-CpG-binding protein 2 isoform X2

  5. XM_047442118.1XP_047298074.1  methyl-CpG-binding protein 2 isoform X2

  6. XM_024452383.2XP_024308151.1  methyl-CpG-binding protein 2 isoform X2

    Conserved Domains (1) summary
    smart00391
    Location:176
    MBD; Methyl-CpG binding domain
  7. XM_047442117.1XP_047298073.1  methyl-CpG-binding protein 2 isoform X2

  8. XM_047442121.1XP_047298077.1  methyl-CpG-binding protein 2 isoform X2

  9. XM_047442122.1XP_047298078.1  methyl-CpG-binding protein 2 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152295254..152371375 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)