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    Dnmt1 DNA methyltransferase (cytosine-5) 1 [ Mus musculus (house mouse) ]

    Gene ID: 13433, updated on 12-Sep-2021

    Summary

    Official Symbol
    Dnmt1provided by MGI
    Official Full Name
    DNA methyltransferase (cytosine-5) 1provided by MGI
    Primary source
    MGI:MGI:94912
    See related
    Ensembl:ENSMUSG00000004099
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    MTa; Dnmt; MCMT; Met1; Cxxc9; MTase; Met-1; Dnmt1o; MommeD; m.MmuI; MommeD2
    Summary
    This gene encodes a methyltransferase that preferentially methylates cytosines of CpG residues in hemimethylated DNA to generate fully methylated CpG base pairs during DNA replication. This enzyme plays roles in diverse cellular processes including cell cycle regulation, DNA repair, and telomere maintenance. The encoded protein is composed of an N-terminal domain with a nuclear localization sequence and replication fork-targeting domain, a DNA-binding CXXC domain, two bromo-adjacent homology domains, and a C-terminal catalytic domain. Mouse embryonic stem cells mutant for this gene are viable, but when introduced into the germ line, cause a recessive lethal phenotype with mutant embryos displaying stunted growth and developmental defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 37.3), thymus adult (RPKM 36.6) and 27 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Dnmt1 in Genome Data Viewer
    Location:
    9 A3; 9 7.66 cM
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (20818501..20871184, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (20907206..20959888, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (20711653..20757317, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 23008 Neighboring gene peter pan homolog Neighboring gene eukaryotic translation initiation factor 3, subunit G Neighboring gene microRNA 7081 Neighboring gene sphingosine-1-phosphate receptor 2 Neighboring gene mitochondrial ribosomal protein L4

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA (cytosine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA (cytosine-5-)-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates TAS
    Traceable Author Statement
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables estrogen receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methyl-CpG binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in C-5 methylation of cytosine IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA hypermethylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within DNA methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation involved in embryo development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation involved in embryo development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within_positive_effect DNA methylation involved in embryo development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within DNA methylation on cytosine IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA methylation on cytosine ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in DNA methylation on cytosine within a CG sequence ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in Ras protein signal transduction ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in S-adenosylmethionine metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cellular response to amino acid stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to transforming growth factor beta stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in gene silencing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in maintenance of DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in maintenance of DNA methylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of histone H3-K9 methylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of vascular associated smooth muscle cell apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA methylation-dependent heterochromatin assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of histone H3-K4 methylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of vascular associated smooth muscle cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of cell population proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in pericentric heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in replication fork IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DNA (cytosine-5)-methyltransferase 1
    Names
    DNA MTase MmuI
    DNA methyltransferase MmuI
    NP_001186360.2
    NP_001186361.1
    NP_001186362.1
    NP_001300940.1
    NP_034196.5
    XP_006510051.1
    XP_011240695.1

    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.

    mRNA and Protein(s)

    1. NM_001199431.1NP_001186360.2  DNA (cytosine-5)-methyltransferase 1 isoform 1

      See identical proteins and their annotated locations for NP_001186360.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1). This variant has two upstream in-frame AUGs but N-terminal sequencing and western analysis from PMID: 9830015 (Table I and Figure 2) support the use of the third in-frame AUG.
      Source sequence(s)
      AF162282, AK147143
      Consensus CDS
      CCDS57655.1
      UniProtKB/Swiss-Prot
      P13864
      UniProtKB/TrEMBL
      Q3UHZ3
      Related
      ENSMUSP00000004202.10, ENSMUST00000004202.17
      Conserved Domains (7) summary
      COG0270
      Location:11411594
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:9691104
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:758881
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:648694
      zf-CXXC; CXXC zinc finger domain
      pfam05029
      Location:124331
      TIMELESS_C; Timeless protein C terminal region
      pfam06464
      Location:16106
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:405540
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    2. NM_001199432.1NP_001186361.1  DNA (cytosine-5)-methyltransferase 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate first exon, which results in the use of a downstream start codon, and an alternate in-frame splice site compared to variant 1. The resulting protein (isoform 3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AF036007, AF162282, AK136213, AK147143
      Consensus CDS
      CCDS57653.1
      UniProtKB/Swiss-Prot
      P13864
      UniProtKB/TrEMBL
      J3QNW0, Q3UHZ3, Q3UWN4
      Related
      ENSMUSP00000136982.2, ENSMUST00000177754.9
      Conserved Domains (6) summary
      COG0270
      Location:10221475
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:850985
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:639762
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:529575
      zf-CXXC; CXXC zinc finger domain
      pfam05029
      Location:106212
      TIMELESS_C; Timeless protein C terminal region
      pfam12047
      Location:286421
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    3. NM_001199433.1NP_001186362.1  DNA (cytosine-5)-methyltransferase 1 isoform 4

      See identical proteins and their annotated locations for NP_001186362.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate first exon, which results in use of a downstream start codon compared to variant 1. The resulting protein (isoform 4) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AF036009, AF175432, AK147143, CK636383
      Consensus CDS
      CCDS57654.1
      UniProtKB/Swiss-Prot
      P13864
      UniProtKB/TrEMBL
      Q3UHZ3
      Related
      ENSMUSP00000150433.2, ENSMUST00000216540.2
      Conserved Domains (6) summary
      COG0270
      Location:10231476
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:851986
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:640763
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:530576
      zf-CXXC; CXXC zinc finger domain
      pfam05029
      Location:6213
      TIMELESS_C; Timeless protein C terminal region
      pfam12047
      Location:287422
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    4. NM_001314011.1NP_001300940.1  DNA (cytosine-5)-methyltransferase 1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 5, which is longer than isoform 1. This variant has two upstream in-frame AUGs but N-terminal sequencing and western analysis from PMID: 9830015 (Table I and Figure 2) support the use of the third in-frame AUG.
      Source sequence(s)
      AF162282, AK147143, BC053047
      UniProtKB/Swiss-Prot
      P13864
      UniProtKB/TrEMBL
      Q3UHZ3, Q7TSJ0
      Conserved Domains (6) summary
      COG0270
      Location:11481601
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:9761111
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:765888
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:655701
      zf-CXXC; CXXC zinc finger domain
      pfam06464
      Location:16106
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:412547
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    5. NM_010066.4NP_034196.5  DNA (cytosine-5)-methyltransferase 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is one amino acid shorter than isoform 1. This variant has two upstream in-frame AUGs but N-terminal sequencing and western analysis from PMID: 9830015 (Table I and Figure 2) support the use of the third in-frame AUG.
      Source sequence(s)
      AC170598, AF162282, AK147143
      UniProtKB/Swiss-Prot
      P13864
      UniProtKB/TrEMBL
      Q3UHZ3
      Conserved Domains (6) summary
      COG0270
      Location:11401593
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:9681103
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:757880
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:647693
      zf-CXXC; CXXC zinc finger domain
      pfam06464
      Location:16106
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:404539
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      20818501..20871184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006509988.3XP_006510051.1  DNA (cytosine-5)-methyltransferase 1 isoform X1

      Conserved Domains (7) summary
      COG0270
      Location:12001653
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:10281163
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:817940
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:707753
      zf-CXXC; CXXC zinc finger domain
      pfam06464
      Location:69159
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:468597
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
      cl21589
      Location:160353
      Relaxase; Relaxase/Mobilisation nuclease domain
    2. XM_011242393.3XP_011240695.1  DNA (cytosine-5)-methyltransferase 1 isoform X2

      Conserved Domains (6) summary
      PHA03169
      Location:68198
      PHA03169; hypothetical protein; Provisional
      COG0270
      Location:10301483
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:858993
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:647770
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:537583
      zf-CXXC; CXXC zinc finger domain
      pfam12047
      Location:298427
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
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