Human Gene MBD2 (ENST00000256429.8_7) from GENCODE V47lift37
  Description: methyl-CpG binding domain protein 2, transcript variant 1 (from RefSeq NM_003927.5)
Gencode Transcript: ENST00000256429.8_7
Gencode Gene: ENSG00000134046.12_10
Transcript (Including UTRs)
   Position: hg19 chr18:51,677,976-51,751,039 Size: 73,064 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr18:51,686,147-51,750,929 Size: 64,783 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:51,677,976-51,751,039)mRNA (may differ from genome)Protein (411 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MBD2_HUMAN
DESCRIPTION: RecName: Full=Methyl-CpG-binding domain protein 2; AltName: Full=Demethylase; Short=DMTase; AltName: Full=Methyl-CpG-binding protein MBD2;
FUNCTION: Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemimethylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. May enhance the activation of some unmethylated cAMP-responsive promoters.
SUBUNIT: Heterodimer with MBD3. Part of the MeCP1 complex that contains HDAC1 and HDAC2. Binds DNMT1, MIZF, GPN1, SIN3A, GATAD2A/p66-alpha and p66-beta. Interacts with DHX9.
SUBCELLULAR LOCATION: Nucleus. Note=Nuclear, in discrete foci. Detected at replication foci in late S phase.
TISSUE SPECIFICITY: Highly expressed in brain, heart, kidney, stomach, testis and placenta.
SIMILARITY: Contains 1 MBD (methyl-CpG-binding) domain.
CAUTION: Functional studies (PubMed:10050851, PubMed:10950960 and PubMed:12665568) have used a C-terminal fragment of isoform 1 which has been described originally as isoform MBD2b (PubMed:9774669) but cannot however be proven by supporting cDNA sequences.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: MBD2
Diseases sorted by gene-association score: tetralogy of fallot (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 41.25 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 722.67 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -50.10110-0.455 Picture PostScript Text
3' UTR -927.373718-0.249 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016177 - DNA-bd_integrase-typ
IPR025884 - MeCpG-bd_2/3_C_dom
IPR001739 - Methyl_CpG_DNA-bd

Pfam Domains:
PF01429 - Methyl-CpG binding domain
PF14048 - C-terminal domain of methyl-CpG binding protein 2 and 3
PF16564 - p55-binding region of Methyl-CpG-binding domain proteins MBD

SCOP Domains:
54171 - DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2L2L - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UBB5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGD  WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003696 satellite DNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0008327 methyl-CpG binding
GO:0019904 protein domain specific binding
GO:0035197 siRNA binding
GO:0070742 C2H2 zinc finger domain binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000183 chromatin silencing at rDNA
GO:0006346 methylation-dependent chromatin silencing
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007507 heart development
GO:0007568 aging
GO:0009612 response to mechanical stimulus
GO:0014070 response to organic cyclic compound
GO:0030177 positive regulation of Wnt signaling pathway
GO:0031667 response to nutrient levels
GO:0032355 response to estradiol
GO:0034622 cellular macromolecular complex assembly
GO:0035563 positive regulation of chromatin binding
GO:0042127 regulation of cell proliferation
GO:0042711 maternal behavior
GO:0043044 ATP-dependent chromatin remodeling
GO:0044030 regulation of DNA methylation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048568 embryonic organ development
GO:0071407 cellular response to organic cyclic compound

Cellular Component:
GO:0000118 histone deacetylase complex
GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  LF211088 - JP 2014500723-A/18591: Polycomb-Associated Non-Coding RNAs.
LF343925 - JP 2014500723-A/151428: Polycomb-Associated Non-Coding RNAs.
LF343924 - JP 2014500723-A/151427: Polycomb-Associated Non-Coding RNAs.
LF343923 - JP 2014500723-A/151426: Polycomb-Associated Non-Coding RNAs.
AF072252 - Homo sapiens methyl-CpG binding protein MBD2 (MBD2) gene, 3' UTR.
JD506656 - Sequence 487680 from Patent EP1572962.
JD411321 - Sequence 392345 from Patent EP1572962.
JD266696 - Sequence 247720 from Patent EP1572962.
JD510757 - Sequence 491781 from Patent EP1572962.
JD184288 - Sequence 165312 from Patent EP1572962.
AL110266 - Homo sapiens mRNA; cDNA DKFZp586O0821 (from clone DKFZp586O0821).
AF039701 - Homo sapiens antigen NY-CO-41 (NY-CO-41) mRNA, partial cds.
BC032638 - Homo sapiens methyl-CpG binding domain protein 2, mRNA (cDNA clone MGC:45085 IMAGE:5496721), complete cds.
AF072242 - Homo sapiens methyl-CpG binding protein MBD2 (MBD2) mRNA, complete cds.
JD384597 - Sequence 365621 from Patent EP1572962.
JD300692 - Sequence 281716 from Patent EP1572962.
JD273852 - Sequence 254876 from Patent EP1572962.
JD270000 - Sequence 251024 from Patent EP1572962.
JD294927 - Sequence 275951 from Patent EP1572962.
JD045928 - Sequence 26952 from Patent EP1572962.
JD303858 - Sequence 284882 from Patent EP1572962.
JD320395 - Sequence 301419 from Patent EP1572962.
JD326277 - Sequence 307301 from Patent EP1572962.
JD065893 - Sequence 46917 from Patent EP1572962.
JD300357 - Sequence 281381 from Patent EP1572962.
AF072246 - Homo sapiens testis specific methyl-CpG binding protein MBD2 (MBD2) mRNA, partial cds.
JD211479 - Sequence 192503 from Patent EP1572962.
MA579502 - JP 2018138019-A/151428: Polycomb-Associated Non-Coding RNAs.
MA579501 - JP 2018138019-A/151427: Polycomb-Associated Non-Coding RNAs.
MA579500 - JP 2018138019-A/151426: Polycomb-Associated Non-Coding RNAs.
MA446665 - JP 2018138019-A/18591: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UBB5 (Reactome details) participates in the following event(s):

R-HSA-427337 MBD2 binds methylcytosine in chromatin
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000256429.1, ENST00000256429.2, ENST00000256429.3, ENST00000256429.4, ENST00000256429.5, ENST00000256429.6, ENST00000256429.7, MBD2 , MBD2_HUMAN, NM_003927, O95242, Q9UBB5, Q9UIS8, uc317fup.1, uc317fup.2
UCSC ID: ENST00000256429.8_7
RefSeq Accession: NM_003927.5
Protein: Q9UBB5 (aka MBD2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.