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DNMT1 DNA (cytosine-5-)-methyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 1786, updated on 29-Jul-2014
Official Symbol
DNMT1provided by HGNC
Official Full Name
DNA (cytosine-5-)-methyltransferase 1provided by HGNC
Primary source
HGNC:2976
See related
Ensembl:ENSG00000130816; HPRD:00532; MIM:126375; Vega:OTTHUMG00000180397
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
AIM; DNMT; MCMT; CXXC9; HSN1E; ADCADN
Summary
DNA (cytosine-5-)-methyltransferase 1 has a role in the establishment and regulation of tissue-specific patterns of methylated cytosine residues. Aberrant methylation patterns are associated with certain human tumors and developmental abnormalities. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
See DNMT1 in Epigenomics, MapViewer
Location:
19p13.2
Exon count:
42
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 19 NC_000019.10 (10133345..10195079, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10244021..10305783, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene PPAN-P2RY11 readthrough Neighboring gene small nucleolar RNA, C/D box 105B Neighboring gene peter pan homolog (Drosophila) Neighboring gene purinergic receptor P2Y, G-protein coupled, 11 Neighboring gene eukaryotic translation initiation factor 3, subunit G Neighboring gene sphingosine-1-phosphate receptor 2 Neighboring gene microRNA 4322 Neighboring gene mitochondrial ribosomal protein L4

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Cysteine and methionine metabolism, organism-specific biosystem (from KEGG)
    Cysteine and methionine metabolism, organism-specific biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
  • Cysteine and methionine metabolism, conserved biosystem (from KEGG)
    Cysteine and methionine metabolism, conserved biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Methionine degradation, organism-specific biosystem (from KEGG)
    Methionine degradation, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
  • Methionine degradation, conserved biosystem (from KEGG)
    Methionine degradation, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
  • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
    MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • MicroRNAs in cancer, conserved biosystem (from KEGG)
    MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • Negative epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
    Negative epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). About half of the roughl...
  • NoRC negatively regulates rRNA expression, organism-specific biosystem (from REACTOME)
    NoRC negatively regulates rRNA expression, organism-specific biosystemOnly about half of the rRNA gene copies in a cell are expressed. The remaining copies are silenced by modifications to histones and DNA (reviewed in Santoro and Grummt 2001, Grummt 2007, Preuss and P...
  • One Carbon Metabolism, organism-specific biosystem (from WikiPathways)
    One Carbon Metabolism, organism-specific biosystemThis one-carbon metabolism pathway is centered around folate. Folate has two key carbon-carbon double bonds. Saturating one of them yields dihydrofolate (DHF) and adding an additional molecule of hyd...
  • PRC2 methylates histones and DNA, organism-specific biosystem (from REACTOME)
    PRC2 methylates histones and DNA, organism-specific biosystemPolycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di...
  • RB in Cancer, organism-specific biosystem (from WikiPathways)
    RB in Cancer, organism-specific biosystem
    RB in Cancer
  • Regulation of retinoblastoma protein, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of retinoblastoma protein, organism-specific biosystem
    Regulation of retinoblastoma protein
  • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration and one carbon metabolism, organism-specific biosystem
    Trans-sulfuration and one carbon metabolism
  • Trans-sulfuration pathway, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration pathway, organism-specific biosystemTrans-sulfuration pathway, the pathway of production of GSH from S-adenosylmethionine (SAMe). Evidences have been showed that this pathway was perturbed in liver toxicity studies.
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ16293, MGC104992

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA (cytosine-5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
methyl-CpG binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
C-5 methylation of cytosine IEA
Inferred from Electronic Annotation
more info
 
DNA methylation TAS
Traceable Author Statement
more info
PubMed 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
chromatin modification IEA
Inferred from Electronic Annotation
more info
 
gene silencing IEA
Inferred from Electronic Annotation
more info
 
maintenance of DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of histone H3-K9 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H3-K4 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
centromeric heterochromatin IEA
Inferred from Electronic Annotation
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
replication fork IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
DNA (cytosine-5)-methyltransferase 1
Names
DNA (cytosine-5)-methyltransferase 1
m.HsaI
DNA MTase HsaI
DNA methyltransferase HsaI
CXXC-type zinc finger protein 9
NP_001124295.1
NP_001370.1

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_028016.3 

    Range
    41208..102941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_362

mRNA and Protein(s)

  1. NM_001130823.1NP_001124295.1  DNA (cytosine-5)-methyltransferase 1 isoform a

    See proteins identical to NP_001124295.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BC092517, BC126227, DA653750, X63692
    Consensus CDS
    CCDS45958.1
    UniProtKB/TrEMBL
    I6L9H2
    UniProtKB/Swiss-Prot
    P26358
    Related
    ENSP00000352516, OTTHUMP00000264207, ENST00000359526, OTTHUMT00000451169
    Conserved Domains (7) summary
    pfam09755
    Location:20237
    Blast Score: 100
    DUF2046; Uncharacterized conserved protein H4 (DUF2046)
    COG0270
    Location:11541608
    Blast Score: 421
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    cd04711
    Location:9811117
    Blast Score: 740
    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:770893
    Blast Score: 605
    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:661707
    Blast Score: 202
    zf-CXXC; CXXC zinc finger domain
    pfam06464
    Location:16105
    Blast Score: 266
    DMAP_binding; DMAP1-binding Domain
    pfam12047
    Location:415550
    Blast Score: 424
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
  2. NM_001379.2NP_001370.1  DNA (cytosine-5)-methyltransferase 1 isoform b

    See proteins identical to NP_001370.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    BC092517, BC126227, DA653750, X63692
    Consensus CDS
    CCDS12228.1
    UniProtKB/TrEMBL
    I6L9H2
    UniProtKB/Swiss-Prot
    P26358
    Related
    ENSP00000345739, OTTHUMP00000264205, ENST00000340748, OTTHUMT00000451166
    Conserved Domains (6) summary
    COG0270
    Location:11381592
    Blast Score: 421
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    cd04711
    Location:9651101
    Blast Score: 740
    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:754877
    Blast Score: 604
    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:645691
    Blast Score: 202
    zf-CXXC; CXXC zinc finger domain
    pfam06464
    Location:16105
    Blast Score: 266
    DMAP_binding; DMAP1-binding Domain
    pfam12047
    Location:399534
    Blast Score: 424
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000019.10 

    Range
    10133345..10195079
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722681.1XP_006722744.1  

    Conserved Domains (5) summary
    COG0270
    Location:10171471
    Blast Score: 421
    Dcm; Site-specific DNA methylase [DNA replication, recombination, and repair]
    cd04711
    Location:844980
    Blast Score: 738
    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:633756
    Blast Score: 602
    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:524570
    Blast Score: 201
    zf-CXXC; CXXC zinc finger domain
    pfam12047
    Location:278413
    Blast Score: 424
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

Alternate HuRef

Genomic

  1. AC_000151.1 

    Range
    9824670..9886268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018930.2 

    Range
    10244307..10306021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)