Free for academic non-profit institutions. Other users need a Commercial license

Aliases for MBD1 Gene

Aliases for MBD1 Gene

  • Methyl-CpG Binding Domain Protein 1 2 3 5
  • Protein Containing Methyl-CpG-Binding Domain 1 3 4
  • CXXC-Type Zinc Finger Protein 3 3 4
  • CXXC3 3 4
  • PCM1 3 4
  • The Regulator Of Fibroblast Growth Factor 2 (FGF-2) Transcription 3
  • Methyl-CpG Binding Domain Protein 1 Isoform PCM1 3
  • Methyl-CpG-Binding Domain Protein 1 3
  • Methyl-CpG-Binding Protein MBD1 4
  • RFT 3

External Ids for MBD1 Gene

Previous GeneCards Identifiers for MBD1 Gene

  • GC18M047893
  • GC18M047594
  • GC18M046047
  • GC18M046049
  • GC18M047795
  • GC18M044649

Summaries for MBD1 Gene

Entrez Gene Summary for MBD1 Gene

  • The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains multiple domains: MBD at the N-terminus that functions both in binding to methylated DNA and in protein interactions; several CXXC-type zinc finger domains that mediate binding to non-methylated CpG dinucleotides; transcriptional repression domain (TRD) at the C-terminus that is involved in transcription repression and in protein interactions. Numerous alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Feb 2011]

GeneCards Summary for MBD1 Gene

MBD1 (Methyl-CpG Binding Domain Protein 1) is a Protein Coding gene. Diseases associated with MBD1 include Trigeminal Nerve Disease and Trigeminal Neuralgia. Among its related pathways are Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and methyl-CpG binding.

UniProtKB/Swiss-Prot for MBD1 Gene

  • Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone Lys-9 trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.

Gene Wiki entry for MBD1 Gene

Additional gene information for MBD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MBD1 Gene

Genomics for MBD1 Gene

GeneHancer (GH) Regulatory Elements for MBD1 Gene

Promoters and enhancers for MBD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18I050277 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 585 +1.9 1906 5.4 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B MBD1 SMAD4 RPL17 CXXC1 MEX3C ELAC1 CFAP53
GH18I050282 Enhancer 0.6 ENCODE dbSUPER 550.8 -0.9 -932 0.2 ZBTB33 PRDM2 MBD1 CXXC1
GH18I050283 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 50 -4.4 -4382 5 HDGF FOXA2 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF766 CXXC1 SMAD4 RPL17 MBD1 ELAC1 MEX3C CFAP53
GH18I051189 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.7 -912.8 -912787 9.4 HDGF FOXA2 PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 MEX3C LOC105372118 MBD1 SMAD4 PIR40243 GC18P050945
GH18I049485 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.4 +791.9 791908 8.4 MLX FEZF1 DMAP1 YY1 E2F8 ZNF143 SP3 NFYC ZFP41 SSRP1 C18orf32 GC18M049490 GC18M049512 GC18M049515 GC18M049516 PIR54855 PIR54878 PIR56297 SNORD58C SNORD58B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around MBD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MBD1 gene promoter:

Genomic Locations for MBD1 Gene

Genomic Locations for MBD1 Gene
chr18:50,266,623-50,281,774
(GRCh38/hg38)
Size:
15,152 bases
Orientation:
Minus strand
chr18:47,793,252-47,808,144
(GRCh37/hg19)

Genomic View for MBD1 Gene

Genes around MBD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MBD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MBD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MBD1 Gene

Proteins for MBD1 Gene

  • Protein details for MBD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UIS9-MBD1_HUMAN
    Recommended name:
    Methyl-CpG-binding domain protein 1
    Protein Accession:
    Q9UIS9
    Secondary Accessions:
    • A4UTZ0
    • B4DXJ5
    • E9PEC5
    • K7ELI2
    • K7EQZ4
    • K7ESN0
    • O15248
    • O95241
    • Q7Z7B5
    • Q8N4W4
    • Q9UNZ6
    • Q9UNZ7
    • Q9UNZ8
    • Q9UNZ9

    Protein attributes for MBD1 Gene

    Size:
    605 amino acids
    Molecular mass:
    66607 Da
    Quaternary structure:
    • Interacts with the Ten-1 ICD form of TENM1 (By similarity). Interacts with OASL, AFT7IP, AFT7IP2 and BAHD1. Binds CHAF1A and the SUV39H1-CBX5 complex via the MBD domain. Binds MGP via the TRD domain. May be part of the MeCP1 complex. During DNA replication, it recruits SETDB1 to form a S phase-specific complex that facilitates methylation of H3 Lys-9 during replication-coupled chromatin assembly and is at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1.

    Three dimensional structures from OCA and Proteopedia for MBD1 Gene

    Alternative splice isoforms for MBD1 Gene

neXtProt entry for MBD1 Gene

Post-translational modifications for MBD1 Gene

  • Sumoylated with SUMO1 by PIAS1 and PIAS3. Sumoylation affects transcriptional silencing by preventing the interaction with SETDB1. In contrast, sumoylation may increase interaction with AFT7IP.
  • Ubiquitination at posLast=422422

No data available for DME Specific Peptides for MBD1 Gene

Domains & Families for MBD1 Gene

Gene Families for MBD1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for MBD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UIS9

UniProtKB/Swiss-Prot:

MBD1_HUMAN :
  • The methyl-CpG-binding domain (MBD) functions both in binding to methylated DNA and in protein interactions.
Domain:
  • The methyl-CpG-binding domain (MBD) functions both in binding to methylated DNA and in protein interactions.
  • The third CXXC-type zinc finger mediates binding to non-methylated CpG dinucleotides.
  • The transcriptional repression domain (TRD) is involved in transcription repression and in protein interactions.
genes like me logo Genes that share domains with MBD1: view

Function for MBD1 Gene

Molecular function for MBD1 Gene

GENATLAS Biochemistry:
methyl-CpG binding domain protein 1,widely expressed,repressing transcription in a methylation dependent manner
UniProtKB/Swiss-Prot Function:
Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone Lys-9 trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.
UniProtKB/Swiss-Prot Induction:
Up-regulated by interferon.

Phenotypes From GWAS Catalog for MBD1 Gene

Gene Ontology (GO) - Molecular Function for MBD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 9774669
GO:0005515 protein binding IPI 12665582
GO:0008270 zinc ion binding IEA --
GO:0008327 methyl-CpG binding NAS 10454587
GO:0010385 double-stranded methylated DNA binding IDA 11371345
genes like me logo Genes that share ontologies with MBD1: view
genes like me logo Genes that share phenotypes with MBD1: view

Animal Models for MBD1 Gene

MGI Knock Outs for MBD1:

Clone Products

  • Addgene plasmids for MBD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MBD1 Gene

Localization for MBD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD1 Gene

Nucleus. Nucleus matrix. Nucleus speckle. Chromosome. Note=Colocalizes with the Ten-1 ICD form of TENM1 in foci associated with the nuclear matrix (By similarity). Nuclear, in a punctate pattern. Associated with euchromatic regions of the chromosomes, with pericentromeric regions on chromosome 1 and with telomeric regions from several chromosomes. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MBD1 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Vesicles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MBD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 10454587
GO:0005694 chromosome IEA --
GO:0016363 nuclear matrix ISS --
GO:0016607 nuclear speck ISS --
genes like me logo Genes that share ontologies with MBD1: view

Pathways & Interactions for MBD1 Gene

genes like me logo Genes that share pathways with MBD1: view

Pathways by source for MBD1 Gene

Gene Ontology (GO) - Biological Process for MBD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 9774669
GO:0045892 negative regulation of transcription, DNA-templated NAS 10454587
genes like me logo Genes that share ontologies with MBD1: view

No data available for SIGNOR curated interactions for MBD1 Gene

Drugs & Compounds for MBD1 Gene

(2) Additional Compounds for MBD1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Cytosine
  • 4-Amino-2(1H)-pyrimidinone
  • 4-Amino-2-hydroxypyrimidine
  • 4-Amino-2-oxo-1,2-dihydropyrimidine
  • 4-Aminouracil
  • Cytosine
71-30-7
genes like me logo Genes that share compounds with MBD1: view

Transcripts for MBD1 Gene

Unigene Clusters for MBD1 Gene

Methyl-CpG binding domain protein 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for MBD1

Alternative Splicing Database (ASD) splice patterns (SP) for MBD1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b · 13c ^ 14a ·
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - -
SP4: - - - -
SP5: - - - - -
SP6: - - - - - -
SP7: - - - - - -
SP8: - -
SP9: - - -
SP10:
SP11: - - -
SP12: - - - - - - -
SP13:
SP14: - - - - - - - - - - - - - -
SP15:
SP16: -
SP17: - - - - -
SP18:
SP19:
SP20:
SP21: -
SP22: - - -
SP23: - -
SP24: -
SP25:

ExUns: 14b · 14c · 14d ^ 15a · 15b · 15c · 15d ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b · 19c · 19d · 19e · 19f · 19g · 19h ^ 20a · 20b
SP1: - - - -
SP2: - - - -
SP3: - -
SP4: - - - - - - - - - -
SP5: - - - - - - - - - -
SP6: - - - - - -
SP7: - - - - - - - - - - - - - - - - -
SP8:
SP9: - - - - -
SP10: - - - - -
SP11:
SP12:
SP13:
SP14:
SP15: - - -
SP16:
SP17: -
SP18: - - - - - - -
SP19: - - - - - - - - - - - - -
SP20: - - - - - -
SP21:
SP22:
SP23:
SP24:
SP25:

Relevant External Links for MBD1 Gene

GeneLoc Exon Structure for
MBD1
ECgene alternative splicing isoforms for
MBD1

Expression for MBD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MBD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MBD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.9), Placenta (9.1), and Testis (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for MBD1 Gene



Protein tissue co-expression partners for MBD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MBD1 Gene:

MBD1

SOURCE GeneReport for Unigene cluster for MBD1 Gene:

Hs.405610

mRNA Expression by UniProt/SwissProt for MBD1 Gene:

Q9UIS9-MBD1_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for MBD1 Gene

  • Nervous system(4.4)
  • Blood(4.3)
  • Liver(4.3)
  • Eye(2.2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with MBD1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for MBD1 Gene

Orthologs for MBD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for MBD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia MBD1 33 34
  • 99.9 (n)
dog
(Canis familiaris)
Mammalia MBD1 33 34
  • 88.99 (n)
cow
(Bos Taurus)
Mammalia MBD1 33 34
  • 86.51 (n)
mouse
(Mus musculus)
Mammalia Mbd1 33 16 34
  • 78.93 (n)
rat
(Rattus norvegicus)
Mammalia Mbd1 33
  • 77.45 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 62 (a)
OneToMany
-- 34
  • 56 (a)
OneToMany
-- 34
  • 54 (a)
OneToMany
-- 34
  • 31 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia MBD1 34
  • 49 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia MBD1 34
  • 45 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia mbd1-prov 33
zebrafish
(Danio rerio)
Actinopterygii mbd1 34
  • 17 (a)
OneToMany
MBD1 (2 of 2) 34
  • 15 (a)
OneToMany
Species where no ortholog for MBD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for MBD1 Gene

ENSEMBL:
Gene Tree for MBD1 (if available)
TreeFam:
Gene Tree for MBD1 (if available)

Paralogs for MBD1 Gene

No data available for Paralogs for MBD1 Gene

Variants for MBD1 Gene

Sequence variations from dbSNP and Humsavar for MBD1 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs116701586 likely-benign, not specified 50,273,600(-) C/G/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1000043942 -- 50,282,078(-) C/A upstream_transcript_variant
rs1000124255 -- 50,266,475(-) G/A downstream_transcript_variant
rs1000184842 -- 50,278,451(-) T/C intron_variant
rs1000447135 -- 50,283,204(-) A/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for MBD1 Gene

Variant ID Type Subtype PubMed ID
nsv576889 CNV loss 21841781
nsv953541 CNV deletion 24416366

Variation tolerance for MBD1 Gene

Residual Variation Intolerance Score: 5.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.76; 78.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MBD1 Gene

Human Gene Mutation Database (HGMD)
MBD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MBD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MBD1 Gene

Disorders for MBD1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for MBD1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
trigeminal nerve disease
  • trigeminal nerve diseases
trigeminal neuralgia
  • tic douloureux
subacute cutaneous lupus erythematosus
  • lupus erythematosus cutaneous subacute
leprosy 3
  • leprosy, susceptibility to, 3
cranial nerve disease
  • cranial nerve disorder
- elite association - COSMIC cancer census association via MalaCards
Search MBD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MBD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MBD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MBD1 Gene

Publications for MBD1 Gene

  1. Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and Mbd4 genes. (PMID: 10441743) Hendrich B … Bird A (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 2 3 4 22 58
  2. Human BAHD1 promotes heterochromatic gene silencing. (PMID: 19666599) Bierne H … Cossart P (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 4 22 58
  3. Methyl-CpG binding domain 1 gene polymorphisms and lung cancer risk in a Chinese population. (PMID: 18668384) Liu H … Lu D (Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals 2008) 3 22 44 58
  4. Regulation of MBD1-mediated transcriptional repression by SUMO and PIAS proteins. (PMID: 17066076) Lyst MJ … Stancheva I (The EMBO journal 2006) 3 4 22 58
  5. Involvement of SUMO modification in MBD1- and MCAF1-mediated heterochromatin formation. (PMID: 16757475) Uchimura Y … Saitoh H (The Journal of biological chemistry 2006) 3 4 22 58

Products for MBD1 Gene

  • Addgene plasmids for MBD1

Sources for MBD1 Gene