Dnmt1 MGI Mouse Gene Detail - MGI:94912

Symbol

Dnmt1
Name

DNA methyltransferase 1
Synonyms

Cxxc9, Dnmt1o, MommeD2, MTase

Feature Type

protein coding gene
IDs

MGI:94912
NCBI Gene: 13433
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr9:20818501-20871084 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 7.66 cM
Mapping Data

3 experiments

SNPs within 2kb

1464 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_94912	protein coding gene	Chr9:20818501-20871184 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0034432	protein coding gene	Chr9:18075760-18121308 (-)
A/J	MGP_AJ_G0034410	protein coding gene	Chr9:17781831-17827785 (-)
AKR/J	MGP_AKRJ_G0034337	protein coding gene	Chr9:18100683-18146257 (-)
BALB/cJ	MGP_BALBcJ_G0034401	protein coding gene	Chr9:17675242-17725149 (-)
C3H/HeJ	MGP_C3HHeJ_G0034113	protein coding gene	Chr9:18412376-18457957 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0034922	protein coding gene	Chr9:18790327-18849957 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031852	protein coding gene	Chr9:16907026-16960331 (-)
CAST/EiJ	MGP_CASTEiJ_G0033436	protein coding gene	Chr9:18234977-18280737 (-)
CBA/J	MGP_CBAJ_G0034086	protein coding gene	Chr9:19514633-19563382 (-)
DBA/2J	MGP_DBA2J_G0034245	protein coding gene	Chr9:17766376-17811961 (-)
FVB/NJ	MGP_FVBNJ_G0034188	protein coding gene	Chr9:17272595-17318199 (-)
LP/J	MGP_LPJ_G0034330	protein coding gene	Chr9:18256694-18302271 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0034231	protein coding gene	Chr9:21138536-21186436 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0034942	protein coding gene	Chr9:18058514-18103763 (-)
PWK/PhJ	MGP_PWKPhJ_G0033142	protein coding gene	Chr9:17732030-17777825 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0032976	protein coding gene	Chr9:18100971-18146627 (-)
WSB/EiJ	MGP_WSBEiJ_G0033551	protein coding gene	Chr9:17782261-17828760 (-)

Human Ortholog

DNMT1, DNA methyltransferase 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

DNMT1, DNA methyltransferase 1
Synonyms

ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT, m.HsaI
Links

HGNC:2976

NCBI Gene ID: 1786

neXtProt AC: NX_P26358

UniProt: P26358
Chr Location

19p13.2; chr19:10133342-10231286 (-) GRCh38

MGI Vertebrate Homology

Dnmt1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: DNMT1
Protein SuperFamily

DNMT1
Gene Tree

Dnmt1

Diseases

5 with human DNMT1 associations

				Human Disease	Mouse Models
				autosomal dominant cerebellar ataxia, deafness and narcolepsy IDs autosomal dominant cerebellar ataxia, deafness and narcolepsy DOID:0050968 OMIM:604121
				Graves' disease IDs Graves' disease DOID:12361 EFO:0004237 ICD10CM:E05.0 MESH:D006111 NCI:C3071 OMIM:275000 UMLS_CUI:C0018213
				hereditary sensory neuropathy IDs hereditary sensory neuropathy DOID:0050548 MESH:D009477 OMIM:PS162400
				hereditary sensory neuropathy type 1E IDs hereditary sensory neuropathy type 1E DOID:0070158 ICD10CM:G60.8 OMIM:614116 ORDO:456318
				lung non-small cell carcinoma IDs lung non-small cell carcinoma DOID:3908 EFO:0003060 KEGG:05223 MESH:D002289 NCI:C2926 UMLS_CUI:C0007131

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

31 phenotypes from 11 alleles in 8 genetic backgrounds
22 phenotypes from multigenic genotypes
182 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

128
Chemically induced (ENU)

2
Endonuclease-mediated

8
Gene trapped

92
Targeted

26
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

112 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mutations causing partial or severe loss of function were homozygous lethal by embryonic day 9.5, with lack of appropriate genomic imprinting observed at several loci. Heterozygosity for specific mutations in the RFTS domain of the encoded peptide affects learning, memory and behavior.

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All GO Annotations

77
GO References

35

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1995
Tissues

813
cDNA Data

37
Literature Summary

95

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

ZFIN dnmt1

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All Sequences

75
RefSeq

14
UniProt

7
CCDS

CCDS57653.1, CCDS57654.1, CCDS57655.1

Ensembl

ENSMUSG00000004099 (Evidence)
NCBI Gene

13433

			Length	Strain/Species	Flank
genomic	13433	NCBI Gene Model \| MGI Sequence Detail	52584	C57BL/6J	± kb
transcript	NM_001199433	RefSeq \| MGI Sequence Detail	6076	ZRU/MplStud
polypeptide	P13864	UniProt \| EBI \| MGI Sequence Detail	1620	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000006606 DNA (cytosine-5)-methyltransferase 1

(term hierarchy)
PDB

3AV4, 3AV5, 3AV6, 3PT6, 3PT9, 4DA4, 5GUT, 5GUV, 5WY1, 6W8V, 6W8W
EC

2.1.1.37
InterPro Domains

IPR001025 Bromo adjacent homology (BAH) domain

IPR043151 Bromo adjacent homology (BAH) domain superfamily

IPR001525 C-5 cytosine methyltransferase

IPR010506 DMAP1-binding domain

IPR050390 DNA Cytosine-5 Methyltransferase

IPR017198 DNA (cytosine-5)-methyltransferase 1-like

IPR022702 DNA (cytosine-5)-methyltransferase 1, replication foci domain

IPR018117 DNA methylase, C-5 cytosine-specific, active site

IPR031303 DNA methylase, C-5 cytosine-specific, conserved site

IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

IPR002857 Zinc finger, CXXC-type
GlyGen

P13864 4 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (2 sites)

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All nucleic 64

Genomic 2

cDNA 37

Primer pair 21

Other 4

Microarray probesets 5

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MGD-MRK-12204, MGD-MRK-12206, MGD-MRK-8877, MGI:3586536

Summaries

All 402

Developmental Gene Expression 95

Gene Ontology 35

Phenotypes 182
Earliest

J:8054 Markovac J, et al., A component of genetic variation among mice in activity of transmembrane methyltransferase I determined by the H-2 region. Biochem Pharmacol. 1985 Oct 1;34(19):3421-5
Latest

J:354132 Tan J, et al., Pramel15 facilitates zygotic nuclear DNMT1 degradation and DNA demethylation. Nat Commun. 2024 Aug 25;15(1):7310

TSS for Dnmt1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr88346	Chr9:20871081-20871088 (-)	-1 bp
Tssr88345	Chr9:20864134-20864177 (-)	6,928 bp
Tssr88344	Chr9:20864098-20864130 (-)	6,970 bp
Tssr88343	Chr9:20853083-20853094 (-)	17,995 bp
Tssr88342	Chr9:20849395-20849410 (-)	21,681 bp
Tssr88341	Chr9:20837140-20837150 (-)	33,939 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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