Dnmt3b DNA methyltransferase 3 beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dnmt3bprovided by RGD
Official Full Name: DNA methyltransferase 3 betaprovided by RGD
Primary source: RGD:1303274
See related: Ensembl:ENSRNOG00000010625 AllianceGenome:RGD:1303274
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA binding activity; chromatin binding activity; and histone deacetylase binding activity. Involved in several processes, including cellular response to dexamethasone stimulus; cellular response to hyperoxia; and response to alkaloid. Located in cytoplasm and nucleus. Biomarker of anxiety disorder; congenital heart disease; hepatocellular carcinoma; and prostatitis. Human ortholog(s) of this gene implicated in several diseases, including acute myeloid leukemia; autoimmune disease (multiple); carcinoma (multiple); immunodeficiency-centromeric instability-facial anomalies syndrome 1; and thymoma. Orthologous to human DNMT3B (DNA methyltransferase 3 beta). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 61.6), Liver (RPKM 19.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q41

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (162590777..162629313)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (142130588..142169128)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (149131541..149170061)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Identification of Epigenetic Interactions between MicroRNA-30c-5p and DNA Methyltransferases in Neuropathic Pain.
Title: Identification of Epigenetic Interactions between MicroRNA-30c-5p and DNA Methyltransferases in Neuropathic Pain.
Downregulation of ELAVL1 attenuates ferroptosis-induced neuronal impairment in rats with cerebral ischemia/reperfusion via reducing DNMT3B-dependent PINK1 methylation.
Title: Downregulation of ELAVL1 attenuates ferroptosis-induced neuronal impairment in rats with cerebral ischemia/reperfusion via reducing DNMT3B-dependent PINK1 methylation.
DNA methyltransferase 3B deficiency unveils a new pathological mechanism of pulmonary hypertension.
Title: DNA methyltransferase 3B deficiency unveils a new pathological mechanism of pulmonary hypertension.
DNMT3B decreases extracellular matrix degradation and alleviates intervertebral disc degeneration through TRPA1 methylation to inhibit the COX2/YAP axis.
Title: DNMT3B decreases extracellular matrix degradation and alleviates intervertebral disc degeneration through TRPA1 methylation to inhibit the COX2/YAP axis.
Epigenetic Blockade of Hippocampal SOD2 Via DNMT3b-Mediated DNA Methylation: Implications in Mild Traumatic Brain Injury-Induced Persistent Oxidative Damage.
Title: Epigenetic Blockade of Hippocampal SOD2 Via DNMT3b-Mediated DNA Methylation: Implications in Mild Traumatic Brain Injury-Induced Persistent Oxidative Damage.
The authors developed a resistant hepatocyte rat model of liver carcinogenesis showing underexpression of DNMT3a and DNMT3b during the early stages.
Title: DNA methyltransferases 3a and 3b are differentially expressed in the early stages of a rat liver carcinogenesis model.
We have found that during acute inflammatory pain induced by the application of 10% mustard oil on the tongues of rats, levels of DNMT3a and 3b were elevated markedly
Title: Epigenetic regulation of acute inflammatory pain.
High resveratrol downregulated DNMT3b and upregulated primarily tumor suppressive miRNAs in hormone sensitive mammary tumors, but not in matched normal mammary tissue.
Title: Methylation and miRNA effects of resveratrol on mammary tumors vs. normal tissue.

Submit: New GeneRIF Correction

General gene information

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Markers

UniSTS:472909 (e-PCR)
- UniSTS:472909

Dnmt3b (e-PCR), detects polymorphism
- UniSTS:472909

UniSTS:525685 (e-PCR)
- UniSTS:525685

Dnmt3b (e-PCR), detects polymorphism
- UniSTS:525685

UniSTS:525686 (e-PCR)
- UniSTS:525686

Dnmt3b (e-PCR), detects polymorphism
- UniSTS:525686

Dnmt3b (e-PCR), detects polymorphism
- UniSTS:525687

Dnmt3b (e-PCR), detects polymorphism
- UniSTS:525699

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IBA Inferred from Biological aspect of Ancestor more info
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	ISO Inferred from Sequence Orthology more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info
enables lncRNA binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within autosome genomic imprinting	ISO Inferred from Sequence Orthology 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 dexamethasone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to hyperoxia	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within epigenetic programming of gene expression	ISO Inferred from Sequence Orthology more info
involved_in epigenetic programming of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gene silencing by piRNA-directed DNA methylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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 transcription by RNA polymerase II	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 neuron differentiation	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within protein-containing complex localization	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 cocaine	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 hypoxia	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 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	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within retrotransposon silencing by heterochromatin formation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of catalytic complex	ISO Inferred from Sequence Orthology more info
located_in chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA (cytosine-5)-methyltransferase 3B

Names: DNA (cytosine-5-)-methyltransferase 3 beta; DNA methyltransferase 3B

NP_001383278.1

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_001396349.1 → NP_001383278.1 DNA (cytosine-5)-methyltransferase 3B

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A0A8I6AVL3, A6KHW2, F1LQ40, Q1LZ51

Related

ENSRNOP00000096797.1, ENSRNOT00000097170.1

Conserved Domains (3) summary

cd05835
Location:229 → 315

Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

cd11728
Location:416 → 535

ADDz_Dnmt3b; ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b)

cl30459
Location:560 → 742

Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086021.1 Reference GRCr8

Range

162590777..162629313

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001003959.1: Suppressed sequence

Description

NM_001003959.1: This RefSeq was removed because currently there is insufficient support for the transcript. Exon 2 has unsupported non-consensus splice junctions in the UTR.