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    MBD6 methyl-CpG binding domain protein 6 [ Homo sapiens (human) ]

    Gene ID: 114785, updated on 3-Apr-2024

    Summary

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    Official Symbol
    MBD6provided by HGNC
    Official Full Name
    methyl-CpG binding domain protein 6provided by HGNC
    Primary source
    HGNC:HGNC:20445
    See related
    Ensembl:ENSG00000166987 MIM:619458; AllianceGenome:HGNC:20445
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables chromatin binding activity. Located in chromocenter; fibrillar center; and nucleoplasm. Implicated in autism spectrum disorder. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 15.8), spleen (RPKM 15.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q13.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57520715..57531545)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57488889..57498388)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57916607..57923931)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene methionyl-tRNA synthetase 1 Neighboring gene uncharacterized LOC128125814 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57913133-57914094 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:57914069-57915268 Neighboring gene microRNA 6758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57916016-57916975 Neighboring gene DNA damage inducible transcript 3 Neighboring gene microRNA 616 Neighboring gene dynactin subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57944162-57944754 Neighboring gene kinesin family member 5A Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57955995-57956161 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57956855-57957072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6549 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57984713-57985214 Neighboring gene phosphatidylinositol-5-phosphate 4-kinase type 2 gamma

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The Expression of MBD6 Is Associated with Tumor Size in Uterine Leiomyomas. Liang MR, et al. Genet Test Mol Biomarkers, 2019 Aug. PMID 31313936
    2. Mutation and expression of a methyl-binding protein 6 (MBD6) in gastric and colorectal cancers. Choi YJ, et al. Pathol Oncol Res, 2015 Jul. PMID 25638327
    3. MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain. Baymaz HI, et al. Proteomics, 2014 Oct. PMID 24634419
    4. MBD6 is a direct target of Oct4 and controls the stemness and differentiation of adipose tissue-derived stem cells. Jung JS, et al. Cell Mol Life Sci, 2013 Feb. PMID 23052207
    5. Comparative study of methyl-CpG-binding domain proteins. Roloff TC, et al. BMC Genomics, 2003 Jan 16. PMID 12529184, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The decreased expression of the MBD6 protein was correlated with the tumor size of uterine leiomyomas
      Title: The Expression of MBD6 Is Associated with Tumor Size in Uterine Leiomyomas.
    2. Our findings imply that reduced stability and enhanced dynamics of MBD1 or MBD6 is the origin of ATP7B dysfunction in Wilson disease patients with the G85V or G591D mutation.
      Title: Disease-causing point-mutations in metal-binding domains of Wilson disease protein decrease stability and increase structural dynamics.
    3. Frameshift mutations of MBD6 gene is associated with stomach and colorectal cancers.
      Title: Mutation and expression of a methyl-binding protein 6 (MBD6) in gastric and colorectal cancers.
    4. We studied and showed that both MBD5 and MBD6 interact with the mammalian PR-DUB Polycomb protein complex in a mutually exclusive manner, and that the MBD of MBD5 and MBD6 is both necessary and sufficient to mediate this interaction.
      Title: MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain.
    5. This study demonstrates examples of autistic patients carrying alterations in MBD6.
      Title: The expanding role of MBD genes in autism: identification of a MECP2 duplication and novel alterations in MBD5, MBD6, and SETDB1.
    6. MBD6 is regulated by Ago2 via an interaction with Oct4, which alters self-renewal and gene expression in human adipose tissue-derived stem cells.
      Title: MBD6 is a direct target of Oct4 and controls the stemness and differentiation of adipose tissue-derived stem cells.
    7. MBD5 and MBD6 are unlikely to be methyl-binding proteins, yet they may contribute to the formation or function of heterochromatin.
      Title: The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1887

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in chromocenter IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromocenter IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    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
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    methyl-CpG-binding domain protein 6
    Names
    methyl-CpG-binding protein MBD6

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_052897.4 → NP_443129.3  methyl-CpG-binding domain protein 6

      See identical proteins and their annotated locations for NP_443129.3

      Status: VALIDATED

      Source sequence(s)
      AB067474, AC022506, AK056399
      Consensus CDS
      CCDS8944.1
      UniProtKB/Swiss-Prot
      Q8N3M0, Q8NA81, Q96DN6, Q96Q00
      UniProtKB/TrEMBL
      Q6P0P0
      Related
      ENSP00000347896.3, ENST00000355673.8
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      57520715..57531545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011537851.4 → XP_011536153.1  methyl-CpG-binding domain protein 6 isoform X1

      See identical proteins and their annotated locations for XP_011536153.1

      UniProtKB/TrEMBL
      Q6P0P0
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    2. XM_006719218.2 → XP_006719281.1  methyl-CpG-binding domain protein 6 isoform X1

      See identical proteins and their annotated locations for XP_006719281.1

      UniProtKB/TrEMBL
      Q6P0P0
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    3. XM_006719217.2 → XP_006719280.1  methyl-CpG-binding domain protein 6 isoform X1

      See identical proteins and their annotated locations for XP_006719280.1

      UniProtKB/TrEMBL
      Q6P0P0
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    4. XM_047428237.1 → XP_047284193.1  methyl-CpG-binding domain protein 6 isoform X2

      UniProtKB/Swiss-Prot
      Q8N3M0, Q8NA81, Q96DN6, Q96Q00

    5. XM_005268617.3 → XP_005268674.1  methyl-CpG-binding domain protein 6 isoform X1

      See identical proteins and their annotated locations for XP_005268674.1

      UniProtKB/TrEMBL
      Q6P0P0
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    6. XM_005268620.4 → XP_005268677.1  methyl-CpG-binding domain protein 6 isoform X3

      UniProtKB/TrEMBL
      Q6P0P0
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    7. XM_005268618.2 → XP_005268675.1  methyl-CpG-binding domain protein 6 isoform X1

      See identical proteins and their annotated locations for XP_005268675.1

      UniProtKB/TrEMBL
      Q6P0P0
      Conserved Domains (1) summary
      cl00110
      Location:16 → 84
      MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...

    8. XM_047428238.1 → XP_047284194.1  methyl-CpG-binding domain protein 6 isoform X2

      UniProtKB/Swiss-Prot
      Q8N3M0, Q8NA81, Q96DN6, Q96Q00

    RNA

    1. XR_007063031.1 RNA Sequence

    2. XR_007063034.1 RNA Sequence

    3. XR_007063033.1 RNA Sequence

    4. XR_007063029.1 RNA Sequence

    5. XR_007063035.1 RNA Sequence

    6. XR_007063032.1 RNA Sequence

    7. XR_429075.3 RNA Sequence

    8. XR_429073.3 RNA Sequence

    9. XR_429076.3 RNA Sequence

    10. XR_429078.3 RNA Sequence

    11. XR_007063030.1 RNA Sequence

    12. XR_429079.3 RNA Sequence

    13. XR_001748569.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      57488889..57498388
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370988.1 → XP_054226963.1  methyl-CpG-binding domain protein 6 isoform X1

    2. XM_054370992.1 → XP_054226967.1  methyl-CpG-binding domain protein 6 isoform X2

      UniProtKB/Swiss-Prot
      Q8N3M0, Q8NA81, Q96DN6, Q96Q00

    3. XM_054370989.1 → XP_054226964.1  methyl-CpG-binding domain protein 6 isoform X1

    4. XM_054370990.1 → XP_054226965.1  methyl-CpG-binding domain protein 6 isoform X1

    5. XM_054370987.1 → XP_054226962.1  methyl-CpG-binding domain protein 6 isoform X1

    6. XM_054370994.1 → XP_054226969.1  methyl-CpG-binding domain protein 6 isoform X3

    7. XM_054370993.1 → XP_054226968.1  methyl-CpG-binding domain protein 6 isoform X2

      UniProtKB/Swiss-Prot
      Q8N3M0, Q8NA81, Q96DN6, Q96Q00

    8. XM_054370991.1 → XP_054226966.1  methyl-CpG-binding domain protein 6 isoform X1

    RNA

    1. XR_008488519.1 RNA Sequence

    2. XR_008488517.1 RNA Sequence

    3. XR_008488520.1 RNA Sequence

    4. XR_008488511.1 RNA Sequence

    5. XR_008488514.1 RNA Sequence

    6. XR_008488512.1 RNA Sequence

    7. XR_008488513.1 RNA Sequence

    8. XR_008488515.1 RNA Sequence

    9. XR_008488516.1 RNA Sequence

    10. XR_008488518.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96DN6.2 GenPept UniProtKB/Swiss-Prot:Q96DN6

    Gene LinkOut

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