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DNMT1 DNA methyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 1786, updated on 12-Sep-2020

Summary

Official Symbol
DNMT1provided by HGNC
Official Full Name
DNA methyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:2976
See related
Ensembl:ENSG00000130816 MIM:126375
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; m.HsaI
Summary
This gene encodes an enzyme that transfers methyl groups to cytosine nucleotides of genomic DNA. This protein is the major enzyme responsible for maintaining methylation patterns following DNA replication and shows a preference for hemi-methylated DNA. Methylation of DNA is an important component of mammalian epigenetic gene regulation. Aberrant methylation patterns are found in human tumors and associated with developmental abnormalities. Variation in this gene has been associated with cerebellar ataxia, deafness, and narcolepsy, and neuropathy, hereditary sensory, type IE. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression
Broad expression in placenta (RPKM 28.0), lymph node (RPKM 23.6) and 24 other tissues See more
Orthologs

Genomic context

See DNMT1 in Genome Data Viewer
Location:
19p13.2
Exon count:
41
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (10133346..10194953, 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 Sharpr-MPRA regulatory region 3609 Neighboring gene purinergic receptor P2Y11 Neighboring gene eukaryotic translation initiation factor 3 subunit G Neighboring gene origin of replication in DNMT1 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 10 pseudogene Neighboring gene sphingosine-1-phosphate receptor 2 Neighboring gene microRNA 4322

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?

Phenotypes

Associated conditions

Description Tests
Cerebellar ataxia, deafness, and narcolepsy, autosomal dominant
MedGen: C3807295 OMIM: 604121 GeneReviews: Not available
Compare labs
Genome wide analysis of narcolepsy in China implicates novel immune loci and reveals changes in association prior to versus after the 2009 H1N1 influenza pandemic.
GeneReviews: Not available
Hereditary sensory neuropathy type IE Compare labs

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates DNMT1, DNMT3A, and DNMT3B both at the mRNA and protein levels in primary tumors PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: S1PR2

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
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-methyltransferase activity TAS
Traceable Author Statement
more info
 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
methyl-CpG binding IEA
Inferred from Electronic Annotation
more info
 
promoter-specific chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 
DNA methylation involved in embryo development IEA
Inferred from Electronic Annotation
more info
 
Ras protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
chromatin organization 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 gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
negative regulation of histone H3-K9 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of vascular associated smooth muscle cell apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of vascular smooth muscle cell differentiation involved in phenotypic switching IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 
positive regulation of methylation-dependent chromatin silencing IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of vascular smooth muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pericentric heterochromatin IEA
Inferred from Electronic Annotation
more info
 
replication fork IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
DNA (cytosine-5)-methyltransferase 1
Names
CXXC-type zinc finger protein 9
DNA (cytosine-5-)-methyltransferase 1
DNA MTase HsaI
DNA methyltransferase HsaI
NP_001124295.1
NP_001305659.1
NP_001305660.1
NP_001370.1

NCBI Reference Sequences (RefSeq)

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 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001130823.3NP_001124295.1  DNA (cytosine-5)-methyltransferase 1 isoform a

    See identical proteins and their annotated locations for NP_001124295.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as Dnmt1b in PMIDs 10449766 and 10753866) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    BC092517, BC126227, DA653750, X63692
    Consensus CDS
    CCDS45958.1
    UniProtKB/Swiss-Prot
    P26358
    UniProtKB/TrEMBL
    I6L9H2
    Related
    ENSP00000352516.3, ENST00000359526.9
    Conserved Domains (6) summary
    COG0270
    Location:11541608
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd04711
    Location:9811117
    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
    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
    zf-CXXC; CXXC zinc finger domain
    pfam06464
    Location:16105
    DMAP_binding; DMAP1-binding Domain
    pfam12047
    Location:415550
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
  2. NM_001318730.2NP_001305659.1  DNA (cytosine-5)-methyltransferase 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has a shorter 5' UTR, lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AB209413, BC092517, BC126227, BX379258, DA653750, HY245803, X63692
    UniProtKB/Swiss-Prot
    P26358
    UniProtKB/TrEMBL
    I6L9H2, Q59FP7
    Conserved Domains (6) summary
    COG0270
    Location:11381595
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd04711
    Location:9651101
    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
    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
    zf-CXXC; CXXC zinc finger domain
    pfam06464
    Location:16105
    DMAP_binding; DMAP1-binding Domain
    pfam12047
    Location:399534
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
  3. NM_001318731.2NP_001305660.1  DNA (cytosine-5)-methyltransferase 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has a shorter 5' UTR, uses an alternate splice site in the 5' region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus than isoform a.
    Source sequence(s)
    BC092517, BX379258, DA653750, X63692
    UniProtKB/Swiss-Prot
    P26358
    UniProtKB/TrEMBL
    I6L9H2
    Conserved Domains (5) summary
    COG0270
    Location:10331487
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd04711
    Location:860996
    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:649772
    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:540586
    zf-CXXC; CXXC zinc finger domain
    pfam12047
    Location:294429
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
  4. NM_001379.4NP_001370.1  DNA (cytosine-5)-methyltransferase 1 isoform b

    See identical proteins and their annotated locations for NP_001370.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as Dnmt1a in PMIDs 10449766 and 10753866) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) is shorter than isoform a.
    Source sequence(s)
    BC092517, BC126227, DA653750, X63692
    Consensus CDS
    CCDS12228.1
    UniProtKB/Swiss-Prot
    P26358
    UniProtKB/TrEMBL
    I6L9H2
    Related
    ENSP00000345739.3, ENST00000340748.8
    Conserved Domains (6) summary
    COG0270
    Location:11381592
    Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
    cd04711
    Location:9651101
    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
    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
    zf-CXXC; CXXC zinc finger domain
    pfam06464
    Location:16105
    DMAP_binding; DMAP1-binding Domain
    pfam12047
    Location:399534
    DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    10133346..10194953 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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