Human Gene DNMT1 (uc010xlc.2)
  Description: Homo sapiens DNA (cytosine-5-)-methyltransferase 1 (DNMT1), transcript variant 1, mRNA.
RefSeq Summary (NM_001130823): 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].
Transcript (Including UTRs)
   Position: hg19 chr19:10,244,022-10,305,755 Size: 61,734 Total Exon Count: 41 Strand: -
Coding Region
   Position: hg19 chr19:10,244,343-10,305,575 Size: 61,233 Coding Exon Count: 41 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:10,244,022-10,305,755)mRNA (may differ from genome)Protein (1632 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DNMT1
CDC HuGE Published Literature: DNMT1

-  MalaCards Disease Associations
  MalaCards Gene Search: DNMT1
Diseases sorted by gene-association score: neuropathy, hereditary sensory, type ie* (1669), cerebellar ataxia, deafness, and narcolepsy, autosomal dominant* (1587), dnmt1-related dementia, deafness, and sensory neuropathy* (500), hereditary sensory and autonomic neuropathy type 1e* (283), narcolepsy (24), cerebellar ataxia (18), systemic lupus erythematosus 15 (13), immunodeficiency-centromeric instability-facial anomalies syndrome (11), neuropathy (8), ataxia (5), colorectal cancer (5), mutagen sensitivity (5), myelodysplastic syndrome (4), ectopic cushing syndrome (4), bipolar disorder (4), lung cancer (3), hematologic cancer (3), nasopharyngeal carcinoma (3), hepatocellular carcinoma (2), mood disorder (2), testicular germ cell tumor (2), schizophrenia (1), leukemia, acute myeloid (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.47 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 453.42 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -61.30180-0.341 Picture PostScript Text
3' UTR -65.25321-0.203 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00145 - C-5 cytosine-specific DNA methylase
PF01426 - BAH domain
PF02008 - CXXC zinc finger domain
PF06464 - DMAP1-binding Domain
PF12047 - Cytosine specific DNA methyltransferase replication foci domain

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on P26358-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK122759 - Homo sapiens cDNA FLJ16293 fis, clone OCBBF2021518, highly similar to DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37).
BC092517 - Homo sapiens DNA (cytosine-5-)-methyltransferase 1, mRNA (cDNA clone MGC:104992 IMAGE:3077831), complete cds.
LF384518 - JP 2014500723-A/192021: Polycomb-Associated Non-Coding RNAs.
AF180682 - Homo sapiens DNA (cytosine-5)-methyltransferase mRNA, complete cds.
X63692 - H.sapiens mRNA for DNA (cytosin-5)-methyltransferase.
AB209413 - Homo sapiens mRNA for DNA (cytosine-5-)-methyltransferase 1 variant, partial cds.
JD500579 - Sequence 481603 from Patent EP1572962.
JD283861 - Sequence 264885 from Patent EP1572962.
BC126227 - Homo sapiens DNA (cytosine-5-)-methyltransferase 1, mRNA (cDNA clone MGC:161505 IMAGE:8991943), complete cds.
BC144093 - Homo sapiens DNA (cytosine-5-)-methyltransferase 1, mRNA (cDNA clone MGC:177630 IMAGE:9052613), complete cds.
JD324054 - Sequence 305078 from Patent EP1572962.
AB384943 - Synthetic construct DNA, clone: pF1KB4396, Homo sapiens DNMT1 gene for DNA (cytosine-5)-methyltransferase 1, complete cds, without stop codon, in Flexi system.
LF375726 - JP 2014500723-A/183229: Polycomb-Associated Non-Coding RNAs.
LF375727 - JP 2014500723-A/183230: Polycomb-Associated Non-Coding RNAs.
LF375728 - JP 2014500723-A/183231: Polycomb-Associated Non-Coding RNAs.
LF375729 - JP 2014500723-A/183232: Polycomb-Associated Non-Coding RNAs.
LF375731 - JP 2014500723-A/183234: Polycomb-Associated Non-Coding RNAs.
LF375732 - JP 2014500723-A/183235: Polycomb-Associated Non-Coding RNAs.
LF375733 - JP 2014500723-A/183236: Polycomb-Associated Non-Coding RNAs.
LF375734 - JP 2014500723-A/183237: Polycomb-Associated Non-Coding RNAs.
LF375735 - JP 2014500723-A/183238: Polycomb-Associated Non-Coding RNAs.
LF375736 - JP 2014500723-A/183239: Polycomb-Associated Non-Coding RNAs.
LF375737 - JP 2014500723-A/183240: Polycomb-Associated Non-Coding RNAs.
LF375738 - JP 2014500723-A/183241: Polycomb-Associated Non-Coding RNAs.
LF375739 - JP 2014500723-A/183242: Polycomb-Associated Non-Coding RNAs.
LF375740 - JP 2014500723-A/183243: Polycomb-Associated Non-Coding RNAs.
LF375741 - JP 2014500723-A/183244: Polycomb-Associated Non-Coding RNAs.
LF375742 - JP 2014500723-A/183245: Polycomb-Associated Non-Coding RNAs.
LF375743 - JP 2014500723-A/183246: Polycomb-Associated Non-Coding RNAs.
LF375745 - JP 2014500723-A/183248: Polycomb-Associated Non-Coding RNAs.
LF375746 - JP 2014500723-A/183249: Polycomb-Associated Non-Coding RNAs.
AY927518 - Homo sapiens mRNA sequence.
LF375748 - JP 2014500723-A/183251: Polycomb-Associated Non-Coding RNAs.
LF375750 - JP 2014500723-A/183253: Polycomb-Associated Non-Coding RNAs.
LF375751 - JP 2014500723-A/183254: Polycomb-Associated Non-Coding RNAs.
LF375752 - JP 2014500723-A/183255: Polycomb-Associated Non-Coding RNAs.
LF375753 - JP 2014500723-A/183256: Polycomb-Associated Non-Coding RNAs.
AF290894 - Homo sapiens DNA (cytosine-5) methyltransferase isoform 1C (DNMT1) mRNA, partial sequence, alternatively spliced.
LF375754 - JP 2014500723-A/183257: Polycomb-Associated Non-Coding RNAs.
LF375755 - JP 2014500723-A/183258: Polycomb-Associated Non-Coding RNAs.
LF375756 - JP 2014500723-A/183259: Polycomb-Associated Non-Coding RNAs.
JD129472 - Sequence 110496 from Patent EP1572962.
MA620095 - JP 2018138019-A/192021: Polycomb-Associated Non-Coding RNAs.
MA611303 - JP 2018138019-A/183229: Polycomb-Associated Non-Coding RNAs.
MA611304 - JP 2018138019-A/183230: Polycomb-Associated Non-Coding RNAs.
MA611305 - JP 2018138019-A/183231: Polycomb-Associated Non-Coding RNAs.
MA611306 - JP 2018138019-A/183232: Polycomb-Associated Non-Coding RNAs.
MA611308 - JP 2018138019-A/183234: Polycomb-Associated Non-Coding RNAs.
MA611309 - JP 2018138019-A/183235: Polycomb-Associated Non-Coding RNAs.
MA611310 - JP 2018138019-A/183236: Polycomb-Associated Non-Coding RNAs.
MA611311 - JP 2018138019-A/183237: Polycomb-Associated Non-Coding RNAs.
MA611312 - JP 2018138019-A/183238: Polycomb-Associated Non-Coding RNAs.
MA611313 - JP 2018138019-A/183239: Polycomb-Associated Non-Coding RNAs.
MA611314 - JP 2018138019-A/183240: Polycomb-Associated Non-Coding RNAs.
MA611315 - JP 2018138019-A/183241: Polycomb-Associated Non-Coding RNAs.
MA611316 - JP 2018138019-A/183242: Polycomb-Associated Non-Coding RNAs.
MA611317 - JP 2018138019-A/183243: Polycomb-Associated Non-Coding RNAs.
MA611318 - JP 2018138019-A/183244: Polycomb-Associated Non-Coding RNAs.
MA611319 - JP 2018138019-A/183245: Polycomb-Associated Non-Coding RNAs.
MA611320 - JP 2018138019-A/183246: Polycomb-Associated Non-Coding RNAs.
MA611322 - JP 2018138019-A/183248: Polycomb-Associated Non-Coding RNAs.
MA611323 - JP 2018138019-A/183249: Polycomb-Associated Non-Coding RNAs.
MA611325 - JP 2018138019-A/183251: Polycomb-Associated Non-Coding RNAs.
MA611327 - JP 2018138019-A/183253: Polycomb-Associated Non-Coding RNAs.
MA611328 - JP 2018138019-A/183254: Polycomb-Associated Non-Coding RNAs.
MA611329 - JP 2018138019-A/183255: Polycomb-Associated Non-Coding RNAs.
MA611330 - JP 2018138019-A/183256: Polycomb-Associated Non-Coding RNAs.
MA611331 - JP 2018138019-A/183257: Polycomb-Associated Non-Coding RNAs.
MA611332 - JP 2018138019-A/183258: Polycomb-Associated Non-Coding RNAs.
MA611333 - JP 2018138019-A/183259: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00270 - Cysteine and methionine metabolism
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein P26358 (Reactome details) participates in the following event(s):

R-HSA-427409 Nucleolar Remodelling Complex (NoRC) binds intergenic region of rDNA
R-HSA-5334160 UHRF1:Chromatin binds DNMT1
R-HSA-212222 PRC2 recruits DNA methyltransferases
R-HSA-5334151 DNMT1 methylates cytosine in hemimethylated DNA
R-HSA-5227490 NoRC:HDAC:DNMT methylates cytosine of the rRNA genes
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-5334118 DNA methylation
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: AIM, CXXC9, DNMT, NM_001130823, NP_001124295, P26358-2
UCSC ID: uc010xlc.2
RefSeq Accession: NM_001130823
Protein: P26358-2, splice isoform of P26358 CCDS: CCDS12228.1, CCDS45958.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DNMT1:
dnmt1-ddsn (DNMT1-Related Disorder)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001130823.1
exon count: 41CDS single in 3' UTR: no RNA size: 5425
ORF size: 4899CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9432.00frame shift in genome: no % Coverage: 99.54
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.