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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
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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)

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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.

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