Dnmt3a Gene Detail

Summary

• Symbol
  Dnmt3a
• Name
  DNA methyltransferase 3A

• Feature Type
  protein coding gene
• IDs
  MGI:1261827
  NCBI Gene: 13435
• Alliance
  gene page
• Transcription Start Sites
  42 TSS

Location &
Maps

• Sequence Map
  Chr12:3856007-3964443 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 12, 1.99 cM, cytoband A2-A3
• Mapping Data
  3 experiments

Strain
Comparison

• SNPs within 2kb
  2312 from dbSNP Build 142
• Strain Annotations
  17

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1261827	protein coding gene	Chr12:3851559-3964443 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019559	protein coding gene	Chr12:640910-750957 (+)
A/J	MGP_AJ_G0019526	protein coding gene	Chr12:679760-790171 (+)
AKR/J	MGP_AKRJ_G0019496	protein coding gene	Chr12:818499-932837 (+)
BALB/cJ	MGP_BALBcJ_G0019501	protein coding gene	Chr12:705992-820360 (+)
C3H/HeJ	MGP_C3HHeJ_G0019307	protein coding gene	Chr12:594599-714471 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0019951	protein coding gene	Chr12:653616-773982 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017575	protein coding gene	Chr12:601902-701962 (+)
CAST/EiJ	MGP_CASTEiJ_G0018862	protein coding gene	Chr12:656562-767162 (+)
CBA/J	MGP_CBAJ_G0019278	protein coding gene	Chr12:896128-1007255 (+)
DBA/2J	MGP_DBA2J_G0019391	protein coding gene	Chr12:623938-732768 (+)
FVB/NJ	MGP_FVBNJ_G0019382	protein coding gene	Chr12:646847-753574 (+)
LP/J	MGP_LPJ_G0019462	protein coding gene	Chr12:665092-770467 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019415	protein coding gene	Chr12:712925-823717 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0019989	protein coding gene	Chr12:595137-711392 (+)
PWK/PhJ	MGP_PWKPhJ_G0018628	protein coding gene	Chr12:632779-739647 (+)
SPRET/EiJ	no annotation
WSB/EiJ	MGP_WSBEiJ_G0018914	protein coding gene	Chr12:630643-740995 (+)

Homology

• Human Ortholog
  DNMT3A, DNA methyltransferase 3 alpha

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  DNMT3A, DNA methyltransferase 3 alpha
  
• Synonyms
  DNMT3A2, HESJAS, M.HsaIIIA, TBRS
• Links
  HGNC:2978

  NCBI Gene ID: 1788

  neXtProt AC: NX_Q9Y6K1

  UniProt: Q9Y6K1

  
  
• Chr Location
  2p23.3; chr2:25227855-25342590 (-)  GRCh38

---

• MGI Vertebrate Homology
  Dnmt3a stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: DNMT3A
• Gene Tree
  Dnmt3a
  

Human Diseases

• Diseases
  6 with human DNMT3A associations

				Human Disease	Mouse Models
				acute lymphoblastic leukemia IDs acute lymphoblastic leukemia       DOID:9952 EFO:0000220 ICD10CM:C91.00 ICD9CM:204.0 NCI:C3167 NCI:C7055 OMIM:247640 OMIM:613065 ORDO:513 UMLS_CUI:C0023449 UMLS_CUI:C1335469
				acute myeloid leukemia IDs acute myeloid leukemia       DOID:9119 DOID:9118 DOID:9171 ICD10CM:C92.0 ICD9CM:205.0 KEGG:05221 MESH:D015470 NCI:C3171 OMIM:601626 UMLS_CUI:C0023467
				myelodysplastic syndrome IDs myelodysplastic syndrome       DOID:0050908 MESH:D009190 OMIM:614286 UMLS_CUI:C2713368
				stomach cancer IDs stomach cancer       DOID:10534 DOID:10539 DOID:10542 DOID:10543 DOID:4713 ICD10CM:C16 ICD10CM:C16.2 ICD10CM:C16.5 ICD10CM:C16.6 ICD9CM:151 ICD9CM:151.4 ICD9CM:151.5 ICD9CM:151.6 ICD9CM:151.9 MESH:D013274 NCI:C3387 NCI:C9331 OMIM:613659 UMLS_CUI:C0024623 UMLS_CUI:C0038356 UMLS_CUI:C0153421 UMLS_CUI:C0153422 UMLS_CUI:C0153423
				T-cell acute lymphoblastic leukemia IDs T-cell acute lymphoblastic leukemia       DOID:5603 MESH:D015458 UMLS_CUI:C0023492
				Tatton-Brown-Rahman syndrome IDs Tatton-Brown-Rahman syndrome       DOID:0112339 OMIM:615879 ORDO:404443

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

• Mutations/Alleles
  1 with disease annotations

• References
  1 with disease annotations

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  38 phenotypes from 9 alleles in 8 genetic backgrounds
  19 phenotypes from multigenic genotypes
  174 phenotype references
  

• All Mutations and Alleles
  102
• Endonuclease-mediated
  9
• Gene trapped
  72
• Targeted
  18
• Transgenic
  3
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  139 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Homozygotes for a targeted null mutation become runted and die around four weeks of age. Homozygosity for mutations affecting unmethylated histone binding results in abnormal maternal imprinting and abnormal pregnancy.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  90
• GO References
  33

Expression

• Assay Results
  1817
• Tissues
  708
• cDNA Data
  36
• Literature Summary
  89

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GENSAT
  GEO
  Expression Atlas
• Other Vertebrate Links
  GEISHA DNMT3A
  Xenbase dnmt3a
  ZFIN dnmt3aa, dnmt3ab

Sequences &
Gene Models

• All Sequences
  113
• RefSeq
  16
• UniProt
  14
• CCDS
  CCDS25784.1, CCDS36397.1

• Ensembl
  ENSMUSG00000020661 (Evidence)
• NCBI Gene
  13435

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000020661	Ensembl Gene Model | MGI Sequence Detail	108437	C57BL/6J
transcript	ENSMUST00000020991	Ensembl | MGI Sequence Detail	9685	Not Applicable
polypeptide	ENSMUSP00000020991	Ensembl | MGI Sequence Detail	908	Not Applicable

Protein
Information

• UniProt
  14 Sequences
• Protein Ontology
  PR:000006607 DNA (cytosine-5)-methyltransferase 3A
  (term hierarchy)
• PDB
  3SW9, 3SWC
• EC
  2.1.1.-, 2.1.1.37
• InterPro Domains
  IPR025766 ADD domain
  IPR001525 C-5 cytosine methyltransferase
  IPR044108 DNA (cytosine-5)-methyltransferase 3A, ADD domain
  IPR018117 DNA methylase, C-5 cytosine-specific, active site
  IPR049554 DNMT3, ADD domain, PHD zinc finger
  IPR040552 DNMT3, cysteine rich ADD domain, GATA1-like zinc finger
  IPR000313 PWWP domain
  IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

Molecular
Reagents

• All nucleic 65

  Genomic 1

  cDNA 38

  Primer pair 25

  Other 1

  
  

  Microarray probesets 8

Other
Accession IDs

MGI:2144939, MGI:2145138

References

• Summaries
  All 379

  Developmental Gene Expression 89

  Diseases 1

  Gene Ontology 33

  Phenotypes 174
• Earliest
  J:48528 Okano M, et al., Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases [letter]. Nat Genet. 1998 Jul;19(3):219-20
• Latest
  J:359345 Bowman RL, et al., In vivo models of subclonal oncogenesis and dependency in hematopoietic malignancy. Cancer Cell. 2024 Nov 11;42(11):1955-1969.e7

TSS for Dnmt3a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr112499	Chr12:3856003-3856031 (+)	10 bp
Tssr112500	Chr12:3856513-3856527 (+)	513 bp
Tssr112501	Chr12:3856536-3856571 (+)	547 bp
Tssr112502	Chr12:3856962-3856973 (+)	961 bp
Tssr112503	Chr12:3857001-3857016 (+)	1,002 bp
Tssr112504	Chr12:3857017-3857063 (+)	1,033 bp
Tssr112505	Chr12:3857076-3857086 (+)	1,074 bp
Tssr112506	Chr12:3876578-3876591 (+)	20,578 bp
Tssr112507	Chr12:3876623-3876635 (+)	20,622 bp
Tssr112508	Chr12:3884789-3884813 (+)	28,794 bp
Tssr112509	Chr12:3884817-3884843 (+)	28,823 bp
Tssr112510	Chr12:3884850-3884864 (+)	28,850 bp
Tssr112511	Chr12:3884874-3884877 (+)	28,869 bp
Tssr112512	Chr12:3884893-3884900 (+)	28,890 bp
Tssr112513	Chr12:3906330-3906350 (+)	50,333 bp
Tssr112514	Chr12:3906395-3906411 (+)	50,396 bp
Tssr112515	Chr12:3910980-3910998 (+)	54,982 bp
Tssr112516	Chr12:3911004-3911028 (+)	55,009 bp
Tssr112517	Chr12:3915112-3915119 (+)	59,109 bp
Tssr112518	Chr12:3921355-3921364 (+)	65,353 bp
Tssr112519	Chr12:3923084-3923101 (+)	67,086 bp
Tssr112520	Chr12:3923103-3923120 (+)	67,105 bp
Tssr112521	Chr12:3923135-3923145 (+)	67,133 bp
Tssr112522	Chr12:3923165-3923175 (+)	67,163 bp
Tssr112523	Chr12:3936008-3936013 (+)	80,004 bp
Tssr112524	Chr12:3941308-3941358 (+)	85,326 bp
Tssr112525	Chr12:3941753-3941801 (+)	85,770 bp
Tssr112526	Chr12:3941810-3941829 (+)	85,813 bp
Tssr112527	Chr12:3944798-3944864 (+)	88,824 bp
Tssr112528	Chr12:3944881-3944896 (+)	88,882 bp
Tssr112529	Chr12:3945468-3945487 (+)	89,471 bp
Tssr112530	Chr12:3947384-3947396 (+)	91,383 bp
Tssr112531	Chr12:3947405-3947436 (+)	91,414 bp
Tssr112532	Chr12:3954188-3954200 (+)	98,187 bp
Tssr112533	Chr12:3955352-3955353 (+)	99,346 bp
Tssr112534	Chr12:3956808-3956821 (+)	100,808 bp
Tssr112535	Chr12:3957602-3957619 (+)	101,604 bp
Tssr112536	Chr12:3957673-3957705 (+)	101,682 bp
Tssr112537	Chr12:3957746-3957766 (+)	101,749 bp
Tssr112538	Chr12:3958220-3958229 (+)	102,218 bp
Tssr112539	Chr12:3963160-3963183 (+)	107,165 bp
Tssr112540	Chr12:3963394-3963414 (+)	107,397 bp