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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

MBD6 Gene

protein-coding   GIFtS: 47
GCID: GC12P057916

methyl-CpG binding domain protein 6

  Search for MBD6
in our new
 Human Malady Compendium 
Biological research products
for MBD6
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Methyl-CpG Binding Domain Protein 61 2
KIAA18871 3
Methyl-CpG-Binding Protein MBD62 3
Methyl-CpG-Binding Domain Protein 62

External Ids:    HGNC: 204451   Entrez Gene: 1147852   Ensembl: ENSG000001669877   UniProtKB: Q96DN63   

Export aliases for MBD6 gene to outside databases

Previous GC identifers: GC12P058059 GC12P057633 GC12P056202 GC12P054932


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: MBD6_HUMAN, Q96DN6
Function: Binds to heterochromatin. Does not interact with either methylated or unmethylated DNA (in vitro)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the MBD6 gene promoter:
         Max1   PPAR-gamma1   PPAR-gamma2   c-Myc   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): MBD6 promoter sequence
   Search SABiosciences Chromatin IP Primers for MBD6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat MBD6


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Ensembl cytogenetic band:  12q13.3   HGNC cytogenetic band: 12q13.2

MBD6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MBD6 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P057916:  view genomic region     (about GC identifiers)

Start:
57,914,493 bp from pter      End:
57,923,931 bp from pter
Size:
9,439 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: MBD6_HUMAN, Q96DN6 (See protein sequence)
Recommended Name: Methyl-CpG-binding domain protein 6  
Size: 1003 amino acids; 101201 Da
Subcellular location: Nucleus. Chromosome. Note=Associated with pericentric heterochromatin in about 25% of the cells
Secondary accessions: Q8N3M0 Q8NA81 Q96Q00

Explore the universe of human proteins at neXtProt for MBD6: NX_Q96DN6

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96DN6

  • MBD6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_443129.3  
    ENSEMBL proteins: 
     ENSP00000448070   ENSP00000450370   ENSP00000449603   ENSP00000347896   ENSP00000448202  
     ENSP00000446481   ENSP00000447365   ENSP00000449541   ENSP00000446834   ENSP00000449749  
     ENSP00000450160   ENSP00000447418   ENSP00000390211  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for MBD6

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005694chromosome IEA--
    GO:0005730NOT nucleolus IDA--


    MBD6 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    MBD6 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR001739 Methyl_CpG_DNA-bd

    Graphical View of Domain Structure for InterPro Entry Q96DN6

    ProtoNet protein and cluster: Q96DN6

    UniProtKB/Swiss-Prot: MBD6_HUMAN, Q96DN6
    Domain: The MBD domain is necessary for chromocentric localization
    Similarity: Contains 1 MBD (methyl-CpG-binding) domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: MBD6_HUMAN, Q96DN6
    Function: Binds to heterochromatin. Does not interact with either methylated or unmethylated DNA (in vitro)

    miRNA
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    hsa-miR-579 hsa-miR-607 hsa-miR-1321 hsa-miR-631 hsa-miR-30d hsa-miR-3653 hsa-miR-3921 hsa-miR-3916
    SwitchGear 3'UTR luciferase reporter plasmidMBD6 3' UTR sequence
    Inhib. RNA
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    Clone
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MBD6

    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677NOT DNA binding IDA--
    GO:0003682chromatin binding IDA--


    MBD6 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for MBD6

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for MBD6 (Q96DN62, 3 ENSP000003478964) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DUSP12Q9UNI62, 3, ENSP000003569204MINT-65783 I2D: score=5 STRING: ENSP00000356920
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    DUSP1ENSP000002392234STRING: ENSP00000239223
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for MBD6
    Search CenterWatch for drugs/clinical trials and news about MBD6 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for MBD6 gene: 
    NM_052897.3  

    Unigene Cluster for MBD6:

    Methyl-CpG binding domain protein 6
    Hs.524523  [show with all ESTs]
    Unigene Representative Sequence: NM_052897
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000548887 ENST00000551351 ENST00000549231 ENST00000546805 ENST00000355673(uc001soj.1 uc001sok.1 uc001sol.1)
    ENST00000546632 ENST00000549623 ENST00000552255 ENST00000549042 ENST00000552659
    ENST00000547545 ENST00000548550 ENST00000552163 ENST00000547844 ENST00000431731


    miRNA
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    8/95 QIAGEN miScript miRNA Assays for microRNAs that regulate MBD6 (see all 95):
    hsa-miR-579 hsa-miR-607 hsa-miR-1321 hsa-miR-631 hsa-miR-30d hsa-miR-3653 hsa-miR-3921 hsa-miR-3916
    SwitchGear 3'UTR luciferase reporter plasmidMBD6 3' UTR sequence
    Inhib. RNA
    Products:
         
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    Browse OriGene siRNA
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    Clone
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    Additional cDNA sequence: 

    AB067474.1 AK056399.1 AK093078.1 AK296990.1 AL834230.1 BC034295.1 BC040149.1 BC051370.1 
    BC065530.1 CR627478.1 

    20 DOTS entries:

    DT.121174597  DT.416114  DT.100788549  DT.100884095  DT.97847009  DT.100028132  DT.100673382  DT.121174537 
    DT.121174578  DT.101972327  DT.121174370  DT.121174522  DT.121174551  DT.121174553  DT.121174584  DT.92403881 
    DT.100884101  DT.101975158  DT.91909957  DT.95273168 

    24/247 AceView cDNA sequences (see all 247):

    BQ691135 AW269588 AW518868 CB155693 AX747907 AI357832 BQ022813 CA412667 
    CF272472 BI335776 AI682919 AL834230 BE019241 BC040149 AW449936 CA392636 
    BE466452 BU553233 AA905467 AI337023 BF058702 AB067474 BU902130 AA961062 

    GeneLoc Exon Structure

    5/18 Alternative Splicing Database (ASD) splice patterns (SP) for MBD6 (see all 18)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13a ·
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                      -                       -                                                                                             
    SP4:                                      -     -                 -                                                                                             
    SP5:                                                              -                                                                                             

    ExUns: 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19a · 19b · 19c
    SP1:                                                                  
    SP2:                                                                  
    SP3:                                                                  
    SP4:                                                                  
    SP5:                                                                  


    ECgene alternative splicing isoforms for MBD6

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    MBD6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ACCAGCTGTC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See MBD6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for MBD6

    SOURCE GeneReport for Unigene cluster: Hs.524523
        SABiosciences Custom PCR Arrays for MBD6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MBD6

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for MBD6 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Mbd61 , 5 methyl-CpG binding domain protein 61, 5 92.11(n)1
    93.98(a)1
      10 (74.50 cM)5
    1109621  NM_033072.21  NP_149063.21 
     1272819565 
    lizard
    (Anolis carolinensis)
    Reptilia MBD66
    --
    37(a)
    1 ↔ 1
    GL343212.1(515986-546851)
    zebrafish
    (Danio rerio)
    Actinopterygii mbd61 methyl-CpG binding domain protein 6 43.81(n)
    36.87(a)
      561863  XM_685268.3  XP_690360.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta sba6
    six-banded
    10(a)
    1 → many
    3R(19719889-19748695)


    ENSEMBL Gene Tree for MBD6 (if available)
    TreeFam Gene Tree for MBD6 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for MBD6 gene
    MBD52  
    2 SIMAP similar genes for MBD6 using alignment to 11 protein entries:     MBD6_HUMAN (see all proteins):
    DKFZp762N1313    MBD5

    MBD6 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/168 NCBI SNPs in MBD6 are shown (see all 168    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1900375751,2
    --57916520(+) GCTCCG/TGCGGC 1 -- us2k10--------
    rs1816989361,2
    --57916542(+) CAGCGA/GCGGCG 1 -- us2k10--------
    rs1853247241,2
    --57916556(+) GCGGCA/GGCGGC 1 -- us2k10--------
    rs1384057751,2
    --57916988(+) CCCACC/TCTCCG 1 -- int10--------
    rs1423270441,2
    --57917187(+) AGGACA/CGGCTC 1 -- int10--------
    rs1902015501,2
    --57917335(+) TATATC/TAGCGA 1 -- int10--------
    rs1819524751,2
    --57917363(+) CATGGG/TGGGAG 1 -- int10--------
    rs1381890901,2
    --57917396(+) GGCAGC/TTGGGC 1 -- int10--------
    rs1437707801,2
    --57917427(+) GGCAAA/TCTGTA 1 -- int10--------
    rs1849422791,2
    --57917443(+) TATATC/TATCTT 1 -- int10--------

    HapMap Linkage Disequilibrium report for MBD6 (57914493 - 57923931 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for MBD6
         1 CNV: 3891

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for MBD6

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    MBD6 for disorders           About MalaCards

    MBD6 for disorders           About GeneDecksing

    1 disease from the University of Copenhagen DISEASES database for MBD6:
    Rett syndrome
    Human Genome Epidemiology (HuGE) Navigator: MBD6 (1 document)

    Export disorders for MBD6 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for MBD6 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with MBD6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The human proteins MBD5 and MBD6 associate with heter ochromatin but they do not bind methylated DNA. (PubMed id 20700456)1, 2 Laget S....Defossez P.A. (2010)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Comparative study of methyl-CpG-binding domain proteins. (PubMed id 12529184)1, 3 Roloff T.C.... Nuber U.A. (2003)
    4. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PubMed id 11572484)1, 2 Nagase T....Ohara O. (2001)
    5. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    8. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (2006)
    9. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)1 Lim J.... Zoghbi H.Y. (2006)
    10. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 114785 HGNC: 20445 AceView: MBD6 Ensembl:ENSG00000166987 euGenes: HUgn114785
    ECgene: MBD6 H-InvDB: MBD6

    (According to HUGE)
    About This Section
    HUGE: KIAA1887

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for MBD6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for MBD6 gene:
    Search GeneIP for patents involving MBD6

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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