Dnmt1 DNA methyltransferase 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Dnmt1provided by MGI
Official Full Name: DNA methyltransferase 1provided by MGI
Primary source: MGI:MGI:94912
See related: Ensembl:ENSMUSG00000004099 AllianceGenome:MGI:94912
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Dnmt; MCMT; Met1; Cxxc9; MTase; Met-1; Dnmt1o; m.MmuI; MommeD2
Summary: This gene encodes a methyltransferase that preferentially methylates cytosines of CpG residues in hemimethylated DNA to generate fully methylated CpG base pairs during DNA replication. This enzyme plays roles in diverse cellular processes including cell cycle regulation, DNA repair, and telomere maintenance. The encoded protein is composed of an N-terminal domain with a nuclear localization sequence and replication fork-targeting domain, a DNA-binding CXXC domain, two bromo-adjacent homology domains, and a C-terminal catalytic domain. Mouse embryonic stem cells mutant for this gene are viable, but when introduced into the germ line, cause a recessive lethal phenotype with mutant embryos displaying stunted growth and developmental defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 37.3), thymus adult (RPKM 36.6) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 A3; 9 7.66 cM

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (20818501..20871084, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (20907206..20959888, complement)

Chromosome 9 - NC_000075.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Obesity promotes the global hypomethylation of CD4+ T cells in patients with systemic lupus erythematosus via downregulating DNMT1.
Title: Obesity promotes the global hypomethylation of CD4+ T cells in patients with systemic lupus erythematosus via downregulating DNMT1.
Pramel15 facilitates zygotic nuclear DNMT1 degradation and DNA demethylation.
Title: Pramel15 facilitates zygotic nuclear DNMT1 degradation and DNA demethylation.
Exploring the role of DNMT1 in dental papilla cell fate specification during mouse tooth germ development through integrated single-cell transcriptomics and bulk RNA sequencing.
Title: Exploring the role of DNMT1 in dental papilla cell fate specification during mouse tooth germ development through integrated single-cell transcriptomics and bulk RNA sequencing.
DNA methyltransferase 1 (DNMT1) promotes cyst growth and epigenetic age acceleration in autosomal dominant polycystic kidney disease.
Title: DNA methyltransferase 1 (DNMT1) promotes cyst growth and epigenetic age acceleration in autosomal dominant polycystic kidney disease.
DNMT1 driven by mouse amniotic fluid mesenchymal stem cell exosomes improved corneal cryoinjury via inducing microRNA-33 promoter DNA hypermethylation modification in corneal epithelium cells.
Title: DNMT1 driven by mouse amniotic fluid mesenchymal stem cell exosomes improved corneal cryoinjury via inducing microRNA-33 promoter DNA hypermethylation modification in corneal epithelium cells.
DNMT1 methylation of LncRNA-ANRIL causes myocardial fibrosis pyroptosis by interfering with the NLRP3/Caspase-1 pathway.
Title: DNMT1 methylation of LncRNA-ANRIL causes myocardial fibrosis pyroptosis by interfering with the NLRP3/Caspase-1 pathway.
Role of LINC00240 on T-helper 9 differentiation in allergic rhinitis through influencing DNMT1-dependent methylation of PU.1.
Title: Role of LINC00240 on T-helper 9 differentiation in allergic rhinitis through influencing DNMT1-dependent methylation of PU.1.
DNMT1 Y495C mutation interferes with maintenance methylation of imprinting control regions.
Title: DNMT1 Y495C mutation interferes with maintenance methylation of imprinting control regions.
Loss of Claudin-1 incurred by DNMT aberration promotes pancreatic cancer progression.
Title: Loss of Claudin-1 incurred by DNMT aberration promotes pancreatic cancer progression.
Knockdown of DNMT1 Induces SLCO3A1 to Promote Follicular Growth by Enhancing the Proliferation of Granulosa Cells in Mammals.
Title: Knockdown of DNMT1 Induces SLCO3A1 to Promote Follicular Growth by Enhancing the Proliferation of Granulosa Cells in Mammals.

Submit: New GeneRIF Correction See all GeneRIFs (258)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (8) 1 citation
Targeted (22) 1 citation

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:516616

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

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:142859

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:142860

PMC133764P2 (e-PCR)
- UniSTS:270655

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

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:472907

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:525682

NoName (e-PCR)
- UniSTS:490614

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:546742

Dnmt1 (e-PCR), detects polymorphism
- UniSTS:526019

Gene Ontology Provided by MGI

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	ISO Inferred from Sequence Orthology more info
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	TAS Traceable Author Statement more info
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates	IEA Inferred from Electronic Annotation more info
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables DNA-methyltransferase activity	TAS Traceable Author Statement more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables lncRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear estrogen receptor binding	ISO Inferred from Sequence Orthology 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 binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to amino acid stimulus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cellular response to bisphenol A	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to transforming growth factor beta stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromosomal DNA methylation maintenance following DNA replication	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within chromosomal DNA methylation maintenance following DNA replication	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within chromosomal DNA methylation maintenance following DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epigenetic programming of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within epigenetic programming of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect epigenetic programming of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
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 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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in female germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement 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
located_in pericentric heterochromatin	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
located_in replication fork	IDA Inferred from Direct Assay more info	PubMed

General protein information

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

Names: DNA MTase MmuI; DNA methyltransferase (cytosine-5) 1; DNA methyltransferase MmuI

NP_001186360.2

EC 2.1.1.37

NP_001186361.1

EC 2.1.1.37

NP_001186362.1

EC 2.1.1.37

NP_001300940.1

EC 2.1.1.37

NP_001391614.2

EC 2.1.1.37

NP_034196.5

EC 2.1.1.37

XP_011240695.1

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_001199431.2 → NP_001186360.2 DNA (cytosine-5)-methyltransferase 1 isoform 1

See identical proteins and their annotated locations for NP_001186360.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest protein (isoform 1). This variant has two upstream in-frame AUGs but N-terminal sequencing and western analysis from PMID: 9830015 (Table I and Figure 2) support the use of the third in-frame AUG.

Source sequence(s)

AC170598

Consensus CDS

CCDS57655.1

UniProtKB/Swiss-Prot

P13864, P97413, Q80ZU3, Q9CSC6, Q9QXX6

UniProtKB/TrEMBL

Q3UHZ3

Related

ENSMUSP00000004202.10, ENSMUST00000004202.17

Conserved Domains (7) summary

COG0270
Location:1141 → 1594

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

cd04711
Location:969 → 1104

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:758 → 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:648 → 694

zf-CXXC; CXXC zinc finger domain

pfam05029
Location:124 → 331

TIMELESS_C; Timeless protein C terminal region

pfam06464
Location:16 → 106

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:405 → 540

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001199432.2 → NP_001186361.1 DNA (cytosine-5)-methyltransferase 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate first exon, which results in the use of a downstream start codon, and an alternate in-frame splice site compared to variant 1. The resulting protein (isoform 3) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC170598

Consensus CDS

CCDS57653.1

UniProtKB/TrEMBL

J3QNW0, Q3UHZ3

Related

ENSMUSP00000136982.2, ENSMUST00000177754.9

Conserved Domains (6) summary

COG0270
Location:1022 → 1475

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

cd04711
Location:850 → 985

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:639 → 762

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:529 → 575

zf-CXXC; CXXC zinc finger domain

pfam05029
Location:106 → 212

TIMELESS_C; Timeless protein C terminal region

pfam12047
Location:286 → 421

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001199433.2 → NP_001186362.1 DNA (cytosine-5)-methyltransferase 1 isoform 4

See identical proteins and their annotated locations for NP_001186362.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate first exon, which results in use of a downstream start codon compared to variant 1. The resulting protein (isoform 4) has a shorter N-terminus than isoform 1.

Source sequence(s)

AC170598

Consensus CDS

CCDS57654.1

UniProtKB/TrEMBL

Q3UHZ3

Related

ENSMUSP00000150433.2, ENSMUST00000216540.2

Conserved Domains (6) summary

COG0270
Location:1023 → 1476

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

cd04711
Location:851 → 986

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:640 → 763

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:530 → 576

zf-CXXC; CXXC zinc finger domain

pfam05029
Location:6 → 213

TIMELESS_C; Timeless protein C terminal region

pfam12047
Location:287 → 422

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001314011.2 → NP_001300940.1 DNA (cytosine-5)-methyltransferase 1 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 5, which is longer than isoform 1. This variant has two upstream in-frame AUGs but N-terminal sequencing and western analysis from PMID: 9830015 (Table I and Figure 2) support the use of the third in-frame AUG.

Source sequence(s)

AC170598

UniProtKB/TrEMBL

Q3UHZ3, Q7TSJ0

Conserved Domains (6) summary

COG0270
Location:1148 → 1601

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

cd04711
Location:976 → 1111

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:765 → 888

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:655 → 701

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:16 → 106

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:412 → 547

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001404685.2 → NP_001391614.2 DNA (cytosine-5)-methyltransferase 1 isoform 6

Status: VALIDATED

Source sequence(s)

AC170598

UniProtKB/TrEMBL

Q3UHZ3
NM_010066.5 → NP_034196.5 DNA (cytosine-5)-methyltransferase 1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is one amino acid shorter than isoform 1. This variant has two upstream in-frame AUGs but N-terminal sequencing and western analysis from PMID: 9830015 (Table I and Figure 2) support the use of the third in-frame AUG.

Source sequence(s)

AC170598

UniProtKB/TrEMBL

Q3UHZ3

Conserved Domains (6) summary

COG0270
Location:1140 → 1593

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

cd04711
Location:968 → 1103

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:757 → 880

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:647 → 693

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:16 → 106

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:404 → 539

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

20818501..20871084 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011242393.3 → XP_011240695.1 DNA (cytosine-5)-methyltransferase 1 isoform X2

UniProtKB/TrEMBL

Q3UHZ3

Conserved Domains (6) summary

PHA03169
Location:68 → 198

PHA03169; hypothetical protein; Provisional

COG0270
Location:1030 → 1483

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

cd04711
Location:858 → 993

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:647 → 770

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:537 → 583

zf-CXXC; CXXC zinc finger domain

pfam12047
Location:298 → 427

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain