Dnmt1 DNA methyltransferase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dnmt1provided by RGD
Official Full Name: DNA methyltransferase 1provided by RGD
Primary source: RGD:620979
See related: Ensembl:ENSRNOG00000039859 AllianceGenome:RGD:620979
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables several functions, including DNA (cytosine-5-)-methyltransferase activity; estrogen receptor binding activity; and histone deacetylase binding activity. Involved in several processes, including DNA metabolic process; cellular response to growth factor stimulus; and nervous system development. Located in cytoplasm; neuronal cell body; and nucleus. Part of protein-containing complex. Used to study choline deficiency disease and lung carcinoma. Biomarker of choline deficiency disease; congenital heart disease; congestive heart failure; liver disease (multiple); and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Graves' disease; autosomal dominant cerebellar ataxia, deafness and narcolepsy; hereditary sensory neuropathy; hereditary sensory neuropathy type 1E; and lung non-small cell carcinoma. Orthologous to human DNMT1 (DNA methyltransferase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 213.6), Spleen (RPKM 125.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q13

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (27716797..27763405, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (19440611..19486659, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (21922515..21968495, complement)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DNMT1 Mediates Chronic Pain-Related Depression by Inhibiting GABAergic Neuronal Activation in the Central Amygdala.
Title: DNMT1 Mediates Chronic Pain-Related Depression by Inhibiting GABAergic Neuronal Activation in the Central Amygdala.
DNMT1-induced miR-133b suppression via methylation promotes myocardial fibrosis after myocardial infarction.
Title: DNMT1-induced miR-133b suppression via methylation promotes myocardial fibrosis after myocardial infarction.
DNMT1 involved in the analgesic effect of folic acid on gastric hypersensitivity through downregulating ASIC1 in adult offspring rats with prenatal maternal stress.
Title: DNMT1 involved in the analgesic effect of folic acid on gastric hypersensitivity through downregulating ASIC1 in adult offspring rats with prenatal maternal stress.
DNMT1 regulates polarization of macrophage-induced intervertebral disc degeneration by modulating SIRT6 expression and promoting pyroptosis in vivo.
Title: DNMT1 regulates polarization of macrophage-induced intervertebral disc degeneration by modulating SIRT6 expression and promoting pyroptosis in vivo.
Runt-related transcription factor 3, mediated by DNA-methyltransferase 1, regulated Schwann cell proliferation and myelination during peripheral nerve regeneration via JAK/STAT signaling pathway.
Title: Runt-related transcription factor 3, mediated by DNA-methyltransferase 1, regulated Schwann cell proliferation and myelination during peripheral nerve regeneration via JAK/STAT signaling pathway.
LncRNA XR_351665 Contributes to Chronic Pain-Induced Depression by Upregulating DNMT1 via Sponging miR-152-3p.
Title: LncRNA XR_351665 Contributes to Chronic Pain-Induced Depression by Upregulating DNMT1 via Sponging miR-152-3p.
A Paternal Methylation Error in the Congenital Hydrocephalic Texas (H-Tx) Rat Is Partially Rescued with Natural Folate Supplements.
Title: A Paternal Methylation Error in the Congenital Hydrocephalic Texas (H-Tx) Rat Is Partially Rescued with Natural Folate Supplements.
RNA interference-mediated silencing of DNA methyltransferase 1 attenuates neuropathic pain by accelerating microglia M2 polarization.
Title: RNA interference-mediated silencing of DNA methyltransferase 1 attenuates neuropathic pain by accelerating microglia M2 polarization.
DNA methyltransferase 1 (DNMT1) suppresses mitophagy and aggravates heart failure via the microRNA-152-3p/ETS1/RhoH axis.
Title: DNA methyltransferase 1 (DNMT1) suppresses mitophagy and aggravates heart failure via the microRNA-152-3p/ETS1/RhoH axis.
DNMT1-Induced miR-152-3p Suppression Facilitates Cardiac Fibroblast Activation in Cardiac Fibrosis.
Title: DNMT1-Induced miR-152-3p Suppression Facilitates Cardiac Fibroblast Activation in Cardiac Fibrosis.

Submit: New GeneRIF Correction See all GeneRIFs (37)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:142858

RH128464 (e-PCR)
- UniSTS:211772

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:472906

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA (cytosine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA (cytosine-5-)-methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables DNA (cytosine-5-)-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables S-adenosylmethionine-dependent methyltransferase activity	TAS Traceable Author Statement more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables lncRNA binding	ISO Inferred from Sequence Orthology more info
enables methyl-CpG binding	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables nuclear estrogen receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to amino acid stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to bisphenol A	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to bisphenol A	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lead ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to nerve growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to platelet-derived growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to transforming growth factor beta stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromosomal DNA methylation maintenance following DNA replication	ISO Inferred from Sequence Orthology more info
involved_in epigenetic programming of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epigenetic programming of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within_positive_effect epigenetic programming of gene expression	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of vascular associated smooth muscle cell apoptotic process	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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 neuron differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular associated smooth muscle cell proliferation	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in response to activity	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to alcohol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to caffeine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to ionizing radiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to lead ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient levels	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic substance	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to testosterone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to toxic substance	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to vitamin A	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in female germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in female germ cell nucleus	ISO Inferred from Sequence Orthology more info
located_in germ cell nucleus	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of pericentric heterochromatin	IEA Inferred from Electronic Annotation more info
part_of pericentric heterochromatin	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in replication fork	IEA Inferred from Electronic Annotation more info
located_in replication fork	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA (cytosine-5)-methyltransferase 1

Names: DNA (cytosine-5-)-methyltransferase 1; DNA MTase RnoIP; DNA methyltransferase (cytosine-5) 1; DNA methyltransferase I; MCMT; m.RnoIP

NP_445806.3

EC 2.1.1.37

XP_063122293.1

EC 2.1.1.37

NCBI Reference Sequences (RefSeq)

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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)

NM_053354.3 → NP_445806.3 DNA (cytosine-5)-methyltransferase 1

See identical proteins and their annotated locations for NP_445806.3

Status: PROVISIONAL

Source sequence(s)

CH473993

UniProtKB/Swiss-Prot

P70487, Q9R252, Q9WTX3, Q9WU57, Q9Z330

UniProtKB/TrEMBL

A6JNM5, F1LQT9

Related

ENSRNOP00000063831.3, ENSRNOT00000064932.5

Conserved Domains (6) summary

COG0270
Location:1142 → 1595

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd04711
Location:969 → 1105

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:759 → 881

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:649 → 695

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:16 → 106

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:405 → 540

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain