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MECP2
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  • MECP2
PROTEIN STRUCTURE
ANTIBODIES
AND
VALIDATION
Protein structures
GENERAL INFORMATIONi

General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.

Gene namei

Official gene symbol, which is typically a short form of the gene name, according to HGNC.

MECP2
Synonyms MRX16, MRX79, RTT
Gene descriptioni

Full gene name according to HGNC.

Methyl-CpG binding protein 2
Protein classi

Assigned HPA protein class(es) for the encoded protein(s).

Read more
Cancer-related genes
Disease related genes
Human disease related genes
Predicted locationi

All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.

  • Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.

  • Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).

The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.

Read more
Intracellular
Protein evidence Evidence at protein level (all genes)
GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Chromosome X
Cytoband q28
Chromosome location (bp) 154021573 - 154137103
Number of transcriptsi

Number of protein-coding transcripts from the gene as defined by Ensembl.

7
Ensembl ENSG00000169057 (version 103.38)
Entrez gene 4204
HGNC HGNC:6990
UniProt P51608 (UniProt - Evidence at protein level)
neXtProt NX_P51608
Antibodypedia MECP2 antibodies


PROTEIN STRUCTUREi

The Structure section provides predicted structures from the Alphafold protein structure database and available experimental structures from Protein Data Bank (PDB).

In the Structure drop-down menu all experimental structures from PDB are available for selection and display. The structures are displayed using the NGL Viewer and can be zoomed-in and rotated either manually or by checking the Autorotate box. The Color scheme can be selected to show the residue index, chain name or confidence score (as B-factors and pLDDT score for experimental and predicted structures, respectively). The positions for available antigen sequences in the structure are shown if Antigens is turned to ON, and the Variants slider can be used to show the positions of clinical and population variants.https://github.com/nglviewer/ngl

Read more

Predicted


Description: Structure prediction from Alphafold project. Structure version 2

# Chains: 1      # Clinical variants: 79      # Population variants: 325

Antigens:

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On

Variants:

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Clinical
Population

Color scheme:

Confidence
Residue index
Chain name

Autorotate:

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On



PROTEIN BROWSERi

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Below the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).

The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
MECP2-201
MECP2-203
MECP2-204
MECP2-205
MECP2-216
MECP2-218
MECP2-223


PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant UniProt Protein class Gene ontology Length & mass Signal peptide
(predicted)
Transmembrane regions
(predicted)
MECP2-201
ENSP00000301948
ENST00000303391
P51608 [Direct mapping]
Methyl-CpG-binding protein 2
D3YJ43 [Target identity:100%; Query identity:100%]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Cancer-related genes
   Candidate cancer biomarkers
Disease related genes
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Mapped to neXtProt
   neXtProt - Evidence at protein level
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0000792 [heterochromatin]
GO:0003677 [DNA binding]
GO:0003682 [chromatin binding]
GO:0003714 [transcription corepressor activity]
GO:0003723 [RNA binding]
GO:0005515 [protein binding]
GO:0005615 [extracellular space]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005813 [centrosome]
GO:0006349 [regulation of gene expression by genetic imprinting]
GO:0006367 [transcription initiation from RNA polymerase II promoter]
GO:0007052 [mitotic spindle organization]
GO:0008284 [positive regulation of cell population proliferation]
GO:0008327 [methyl-CpG binding]
GO:0010385 [double-stranded methylated DNA binding]
GO:0010629 [negative regulation of gene expression]
GO:0010971 [positive regulation of G2/M transition of mitotic cell cycle]
GO:0016525 [negative regulation of angiogenesis]
GO:0019904 [protein domain specific binding]
GO:0042025 [host cell nucleus]
GO:0043537 [negative regulation of blood vessel endothelial cell migration]
GO:0045202 [synapse]
GO:0045892 [negative regulation of transcription, DNA-templated]
GO:0047485 [protein N-terminus binding]
GO:0090063 [positive regulation of microtubule nucleation]
GO:0098794 [postsynapse]
GO:1905643 [positive regulation of DNA methylation]
Show all
486 aa
52.4 kDa
No 0
MECP2-203
ENSP00000384865
ENST00000407218
B5MCB4 [Direct mapping]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0003677 [DNA binding]
GO:0005634 [nucleus]
GO:0010385 [double-stranded methylated DNA binding]
GO:0042025 [host cell nucleus]
Show all
184 aa
20 kDa
No 0
MECP2-204
ENSP00000416267
ENST00000415944
C9JH89 [Direct mapping]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0005634 [nucleus]
GO:0010385 [double-stranded methylated DNA binding]
Show all
49 aa
5.6 kDa
No 0
MECP2-205
ENSP00000395535
ENST00000453960
P51608 [Direct mapping]
Methyl-CpG-binding protein 2
A0A140VKC4 [Target identity:100%; Query identity:100%]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Cancer-related genes
   Candidate cancer biomarkers
Disease related genes
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Mapped to neXtProt
   neXtProt - Evidence at protein level
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0000792 [heterochromatin]
GO:0001662 [behavioral fear response]
GO:0001666 [response to hypoxia]
GO:0001964 [startle response]
GO:0001976 [nervous system process involved in regulation of systemic arterial blood pressure]
GO:0002087 [regulation of respiratory gaseous exchange by nervous system process]
GO:0003677 [DNA binding]
GO:0003682 [chromatin binding]
GO:0003700 [DNA-binding transcription factor activity]
GO:0003714 [transcription corepressor activity]
GO:0003723 [RNA binding]
GO:0003729 [mRNA binding]
GO:0005515 [protein binding]
GO:0005615 [extracellular space]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005813 [centrosome]
GO:0005829 [cytosol]
GO:0006020 [inositol metabolic process]
GO:0006342 [chromatin silencing]
GO:0006349 [regulation of gene expression by genetic imprinting]
GO:0006357 [regulation of transcription by RNA polymerase II]
GO:0006367 [transcription initiation from RNA polymerase II promoter]
GO:0006541 [glutamine metabolic process]
GO:0006576 [cellular biogenic amine metabolic process]
GO:0007052 [mitotic spindle organization]
GO:0007268 [chemical synaptic transmission]
GO:0007416 [synapse assembly]
GO:0007420 [brain development]
GO:0007585 [respiratory gaseous exchange by respiratory system]
GO:0007612 [learning]
GO:0007613 [memory]
GO:0007616 [long-term memory]
GO:0008104 [protein localization]
GO:0008134 [transcription factor binding]
GO:0008211 [glucocorticoid metabolic process]
GO:0008284 [positive regulation of cell population proliferation]
GO:0008327 [methyl-CpG binding]
GO:0008344 [adult locomotory behavior]
GO:0008542 [visual learning]
GO:0009791 [post-embryonic development]
GO:0010385 [double-stranded methylated DNA binding]
GO:0010468 [regulation of gene expression]
GO:0010629 [negative regulation of gene expression]
GO:0010971 [positive regulation of G2/M transition of mitotic cell cycle]
GO:0016358 [dendrite development]
GO:0016525 [negative regulation of angiogenesis]
GO:0016571 [histone methylation]
GO:0016573 [histone acetylation]
GO:0019230 [proprioception]
GO:0019233 [sensory perception of pain]
GO:0019904 [protein domain specific binding]
GO:0021549 [cerebellum development]
GO:0021591 [ventricular system development]
GO:0030182 [neuron differentiation]
GO:0031175 [neuron projection development]
GO:0032048 [cardiolipin metabolic process]
GO:0033555 [multicellular organismal response to stress]
GO:0035176 [social behavior]
GO:0035197 [siRNA binding]
GO:0040029 [regulation of gene expression, epigenetic]
GO:0042025 [host cell nucleus]
GO:0042551 [neuron maturation]
GO:0043524 [negative regulation of neuron apoptotic process]
GO:0043537 [negative regulation of blood vessel endothelial cell migration]
GO:0045202 [synapse]
GO:0045892 [negative regulation of transcription, DNA-templated]
GO:0045893 [positive regulation of transcription, DNA-templated]
GO:0045944 [positive regulation of transcription by RNA polymerase II]
GO:0046470 [phosphatidylcholine metabolic process]
GO:0047485 [protein N-terminus binding]
GO:0048167 [regulation of synaptic plasticity]
GO:0050884 [neuromuscular process controlling posture]
GO:0050905 [neuromuscular process]
GO:0051151 [negative regulation of smooth muscle cell differentiation]
GO:0051570 [regulation of histone H3-K9 methylation]
GO:0051707 [response to other organism]
GO:0060079 [excitatory postsynaptic potential]
GO:0060291 [long-term synaptic potentiation]
GO:0090063 [positive regulation of microtubule nucleation]
GO:0098794 [postsynapse]
GO:1900114 [positive regulation of histone H3-K9 trimethylation]
GO:1905643 [positive regulation of DNA methylation]
GO:1990841 [promoter-specific chromatin binding]
GO:2000820 [negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation]
Show all
498 aa
53.3 kDa
No 0
MECP2-216
ENSP00000486978
ENST00000628176
A0A0D9SFX7 [Direct mapping]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0003677 [DNA binding]
GO:0005634 [nucleus]
GO:0010385 [double-stranded methylated DNA binding]
GO:0042025 [host cell nucleus]
Show all
172 aa
19.1 kDa
No 0
MECP2-218
ENSP00000486089
ENST00000630151
A0A0D9SEX1 [Direct mapping]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Protein evidence (Ezkurdia et al 2014)
Show all
41 aa
4.7 kDa
No 0
MECP2-223
ENSP00000489847
ENST00000637917
A0A1B0GTV0 [Direct mapping]
Methyl-CpG-binding protein 2
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Human disease related genes
   Congenital malformations
   Congenital malformations of the nervous system
   Other diseases
   Mental and behavioural disorders
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0003677 [DNA binding]
GO:0005634 [nucleus]
GO:0010385 [double-stranded methylated DNA binding]
Show all
53 aa
6 kDa
No 0

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