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    MBD5 methyl-CpG binding domain protein 5 [ Homo sapiens (human) ]

    Gene ID: 55777, updated on 23-Nov-2023

    Summary

    Official Symbol
    MBD5provided by HGNC
    Official Full Name
    methyl-CpG binding domain protein 5provided by HGNC
    Primary source
    HGNC:HGNC:20444
    See related
    Ensembl:ENSG00000204406 MIM:611472; AllianceGenome:HGNC:20444
    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
    MRD1; DEL2Q23.1; C2DELq23.1
    Summary
    This gene encodes a member of the methyl-CpG-binding domain (MBD) family. The MBD consists of about 70 residues and is the minimal region required for a methyl-CpG-binding protein binding specifically to methylated DNA. In addition to the MBD domain, this protein contains a PWWP domain (Pro-Trp-Trp-Pro motif), which consists of 100-150 amino acids and is found in numerous proteins that are involved in cell division, growth and differentiation. Mutations in this gene cause an autosomal dominant type of cognitive disability. The encoded protein interacts with the polycomb repressive complex PR-DUB which catalyzes the deubiquitination of a lysine residue of histone 2A. Haploinsufficiency of this gene is associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures. Alternatively spliced transcript variants have been found, but their full-length nature is not determined. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in brain (RPKM 2.6), gall bladder (RPKM 2.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See MBD5 in Genome Data Viewer
    Location:
    2q23.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (148020927..148516971)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (148471381..148967332)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (148778580..149274540)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1275, pseudogene Neighboring gene activin A receptor type 2A Neighboring gene uncharacterized LOC105373674 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:148765513-148766712 Neighboring gene origin recognition complex subunit 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:148777951-148778548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16614 Neighboring gene uncharacterized LOC105373673 Neighboring gene NANOG hESC enhancer GRCh37_chr2:148795224-148795725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16615 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:148946661-148947364 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:149016781-149017980 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene USP12 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149119622-149120160 Neighboring gene ADP ribosylation factor like GTPase 5A pseudogene Neighboring gene uncharacterized LOC124907896 Neighboring gene OCT4 hESC enhancer GRCh37_chr2:149280763-149281300 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:149300377-149300570 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:149311371-149312328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:149317839-149318790 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149335391-149336105 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149336106-149336819 Neighboring gene ribosomal protein S29 pseudogene 8

    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?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ11113, FLJ30517, KIAA1461

    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 
    Process Evidence Code Pubs
    involved_in glucose homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of growth hormone receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of multicellular organism growth ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 extracellular exosome HDA PubMed 
    located_in midbody 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

    Preferred Names
    methyl-CpG-binding domain protein 5
    Names
    methyl-CpG-binding protein MBD5

    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_017003.3 RefSeqGene

      Range
      5166..501046
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001378120.1NP_001365049.1  methyl-CpG-binding domain protein 5 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC016731, AC018465, AC019070, AC019226
      Consensus CDS
      CCDS92873.1
      UniProtKB/TrEMBL
      A0A2R8YDL9
      Related
      ENSP00000493871.2, ENST00000642680.2
      Conserved Domains (2) summary
      cl00110
      Location:2179
      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 ...
      cl02554
      Location:16161693
      PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
    2. NM_018328.5NP_060798.2  methyl-CpG-binding domain protein 5 isoform 2

      See identical proteins and their annotated locations for NP_060798.2

      Status: REVIEWED

      Source sequence(s)
      AC016731, BC150264, DA240785, DB214959
      Consensus CDS
      CCDS33302.1
      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
      Related
      ENSP00000386049.1, ENST00000407073.5
      Conserved Domains (2) summary
      cl00110
      Location:2179
      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 ...
      cl02554
      Location:13831460
      PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      148020927..148516971
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445056.1XP_047301012.1  methyl-CpG-binding domain protein 5 isoform X1

    2. XM_011511472.3XP_011509774.1  methyl-CpG-binding domain protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011509774.1

      Conserved Domains (2) summary
      cd05835
      Location:16161706
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      cl00110
      Location:2179
      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_047445068.1XP_047301024.1  methyl-CpG-binding domain protein 5 isoform X1

    4. XM_047445088.1XP_047301044.1  methyl-CpG-binding domain protein 5 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GW10
    5. XM_047445091.1XP_047301047.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    6. XM_047445058.1XP_047301014.1  methyl-CpG-binding domain protein 5 isoform X1

    7. XM_047445074.1XP_047301030.1  methyl-CpG-binding domain protein 5 isoform X1

    8. XM_047445079.1XP_047301035.1  methyl-CpG-binding domain protein 5 isoform X1

    9. XM_011511470.3XP_011509772.1  methyl-CpG-binding domain protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011509772.1

      Conserved Domains (2) summary
      cd05835
      Location:16161706
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      cl00110
      Location:2179
      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 ...
    10. XM_047445083.1XP_047301039.1  methyl-CpG-binding domain protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDL9
    11. XM_047445090.1XP_047301046.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    12. XM_047445078.1XP_047301034.1  methyl-CpG-binding domain protein 5 isoform X1

    13. XM_047445084.1XP_047301040.1  methyl-CpG-binding domain protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDL9
    14. XM_047445055.1XP_047301011.1  methyl-CpG-binding domain protein 5 isoform X1

    15. XM_047445087.1XP_047301043.1  methyl-CpG-binding domain protein 5 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GW10
      Related
      ENSP00000490728.2, ENST00000638043.2
    16. XM_047445089.1XP_047301045.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    17. XM_047445057.1XP_047301013.1  methyl-CpG-binding domain protein 5 isoform X1

    18. XM_047445085.1XP_047301041.1  methyl-CpG-binding domain protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDL9
    19. XM_024452990.2XP_024308758.1  methyl-CpG-binding domain protein 5 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GW10
      Conserved Domains (2) summary
      cd05835
      Location:13831473
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
      cl00110
      Location:2179
      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 ...
    20. XM_047445092.1XP_047301048.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    21. XM_024452988.2XP_024308756.1  methyl-CpG-binding domain protein 5 isoform X3

      Conserved Domains (2) summary
      cl00110
      Location:2179
      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 ...
      cl02554
      Location:16161692
      PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
    22. XM_024452989.2XP_024308757.1  methyl-CpG-binding domain protein 5 isoform X4

      Conserved Domains (2) summary
      cl00110
      Location:2179
      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 ...
      cl02554
      Location:16161679
      PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
    23. XM_047445063.1XP_047301019.1  methyl-CpG-binding domain protein 5 isoform X1

    24. XM_047445077.1XP_047301033.1  methyl-CpG-binding domain protein 5 isoform X1

    25. XM_047445081.1XP_047301037.1  methyl-CpG-binding domain protein 5 isoform X1

    26. XM_047445082.1XP_047301038.1  methyl-CpG-binding domain protein 5 isoform X1

    27. XM_047445080.1XP_047301036.1  methyl-CpG-binding domain protein 5 isoform X1

    28. XM_047445093.1XP_047301049.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    29. XM_047445086.1XP_047301042.1  methyl-CpG-binding domain protein 5 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      148471381..148967332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342945.1XP_054198920.1  methyl-CpG-binding domain protein 5 isoform X1

    2. XM_054342954.1XP_054198929.1  methyl-CpG-binding domain protein 5 isoform X1

    3. XM_054342949.1XP_054198924.1  methyl-CpG-binding domain protein 5 isoform X1

    4. XM_054342965.1XP_054198940.1  methyl-CpG-binding domain protein 5 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GW10
    5. XM_054342969.1XP_054198944.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    6. XM_054342947.1XP_054198922.1  methyl-CpG-binding domain protein 5 isoform X1

    7. XM_054342950.1XP_054198925.1  methyl-CpG-binding domain protein 5 isoform X1

    8. XM_054342953.1XP_054198928.1  methyl-CpG-binding domain protein 5 isoform X1

    9. XM_054342943.1XP_054198918.1  methyl-CpG-binding domain protein 5 isoform X1

    10. XM_054342958.1XP_054198933.1  methyl-CpG-binding domain protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDL9
    11. XM_054342968.1XP_054198943.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    12. XM_054342952.1XP_054198927.1  methyl-CpG-binding domain protein 5 isoform X1

    13. XM_054342959.1XP_054198934.1  methyl-CpG-binding domain protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDL9
    14. XM_054342944.1XP_054198919.1  methyl-CpG-binding domain protein 5 isoform X1

    15. XM_054342964.1XP_054198939.1  methyl-CpG-binding domain protein 5 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GW10
    16. XM_054342967.1XP_054198942.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    17. XM_054342946.1XP_054198921.1  methyl-CpG-binding domain protein 5 isoform X1

    18. XM_054342960.1XP_054198935.1  methyl-CpG-binding domain protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDL9
    19. XM_054342966.1XP_054198941.1  methyl-CpG-binding domain protein 5 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GW10
    20. XM_054342970.1XP_054198945.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    21. XM_054342961.1XP_054198936.1  methyl-CpG-binding domain protein 5 isoform X3

    22. XM_054342962.1XP_054198937.1  methyl-CpG-binding domain protein 5 isoform X4

    23. XM_054342948.1XP_054198923.1  methyl-CpG-binding domain protein 5 isoform X1

    24. XM_054342951.1XP_054198926.1  methyl-CpG-binding domain protein 5 isoform X1

    25. XM_054342956.1XP_054198931.1  methyl-CpG-binding domain protein 5 isoform X1

    26. XM_054342957.1XP_054198932.1  methyl-CpG-binding domain protein 5 isoform X1

    27. XM_054342955.1XP_054198930.1  methyl-CpG-binding domain protein 5 isoform X1

    28. XM_054342971.1XP_054198946.1  methyl-CpG-binding domain protein 5 isoform X7

      UniProtKB/Swiss-Prot
      A5HMQ4, A7E2B1, Q53SR1, Q9NUV6, Q9P267
    29. XM_054342963.1XP_054198938.1  methyl-CpG-binding domain protein 5 isoform X5