Endometriosis Knowledgebase

Search Result

Gene id

1789

Gene Summary Protein Summary Gene ontology KEGG pathways Diseases PubMed references

Gene Summary

Gene Symbol

DNMT3B Gene UCSC Ensembl

Aliases

ICF, ICF1, M.HsaIIIB

Gene name

DNA methyltransferase 3 beta

Alternate names

DNA (cytosine-5)-methyltransferase 3B, DNA (cytosine-5-)-methyltransferase 3 beta, DNA MTase HsaIIIB, DNA cytosine-5--methyltransferase 3 beta, DNA methyltransferase HsaIIIB,

Gene location

20q11.21 (32762384: 32809355) Exons: 24 NC_000020.11

Gene summary(Entrez)

CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase which is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is developmentally regulated. Mutations in this gene cause the immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined. [provided by RefSeq, May 2011]

OMIM

602900

Protein Summary

Protein general information

Q9UBC3

Name: DNA (cytosine 5) methyltransferase 3B (Dnmt3b) (EC 2.1.1.37) (DNA methyltransferase HsaIIIB) (DNA MTase HsaIIIB) (M.HsaIIIB)

Length: 853 Mass: 95,751

Tissue specificity: Ubiquitous; highly expressed in fetal liver, heart, kidney, placenta, and at lower levels in spleen, colon, brain, liver, small intestine, lung, peripheral blood mononuclear cells, and skeletal muscle. Isoform 1 is expressed in all tis

Sequence

MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREVSSLLSYTQDLTGDGD
GEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPSPRSTRGRQGRNHVDESPVEFPATRSLRRRA
TASAGTPWPSPPSSYLTIDLTDDTEDTHGTPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGI
GDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK
AMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKSKVRRAGSRKLESRKY
ENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLF
EGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCY
MCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK
YVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEF
YHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASK
NDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGA
RQKLLGRSWSVPVIRHLFAPLKDYFACE

Structural information

Protein Domains	PWWP. (225-283) ADD. (423-555) SAM-dependent (575-853)
Interpro:	IPR025766 IPR018117 IPR001525 IPR030488 IPR000313 IPR029063 IPR011011
Prosite:	PS51533 PS00094 PS50812 PS51679
Pfam:	PF00145 PF00855
CDD:	cd11728
PDB:	3FLG 3QKJ 5CIU
PDBsum:	3FLG 3QKJ 5CIU
DIP:	30000
MINT:	2820816
STRING:	ENSP00000328547;

Other Databases

GeneCards: DNMT3B; Malacards: DNMT3B

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0000122	negative regulation of tr anscription from RNA poly merase II promoter	IDA	biological_process
GO:0001666	response to hypoxia	IEA	biological_process
GO:0003682	chromatin binding	IEA	molecular_function
GO:0003714	transcription corepressor activity	IDA	molecular_function
GO:0003714	transcription corepressor activity	IMP	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	TAS	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	NAS	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	IDA	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005634	nucleus	IDA	cellular_component
GO:0005654	nucleoplasm	IDA	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0005737	cytoplasm	IEA	cellular_component
GO:0006306	DNA methylation	TAS	biological_process
GO:0006306	DNA methylation	NAS	biological_process
GO:0006306	DNA methylation	NAS	biological_process
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	TAS	molecular_function
GO:0009636	response to toxic substan ce	IEA	biological_process
GO:0010212	response to ionizing radi ation	IEA	biological_process
GO:0010424	DNA methylation on cytosi ne within a CG sequence	IEA	biological_process
GO:0010628	positive regulation of ge ne expression	IMP	biological_process
GO:0014823	response to activity	IEA	biological_process
GO:0031000	response to caffeine	IEA	biological_process
GO:0032355	response to estradiol	IEA	biological_process
GO:0033189	response to vitamin A	IEA	biological_process
GO:0042220	response to cocaine	IEA	biological_process
GO:0042493	response to drug	IEA	biological_process
GO:0042826	histone deacetylase bindi ng	IEA	molecular_function
GO:0043231	intracellular membrane-bo unded organelle	IDA	cellular_component
GO:0045322	unmethylated CpG binding	IEA	molecular_function
GO:0045666	positive regulation of ne uron differentiation	IEA	biological_process
GO:0045814	negative regulation of ge ne expression, epigenetic	TAS	biological_process
GO:0046498	S-adenosylhomocysteine me tabolic process	IEA	biological_process
GO:0046499	S-adenosylmethioninamine metabolic process	IEA	biological_process
GO:0046872	metal ion binding	IEA	molecular_function
GO:0051571	positive regulation of hi stone H3-K4 methylation	IMP	biological_process
GO:0051573	negative regulation of hi stone H3-K9 methylation	IMP	biological_process
GO:0051718	DNA (cytosine-5-)-methylt ransferase activity, acti ng on CpG substrates	IEA	molecular_function
GO:0071455	cellular response to hype roxia	IEA	biological_process
GO:0071549	cellular response to dexa methasone stimulus	IEA	biological_process
GO:0090116	C-5 methylation of cytosi ne	IEA	biological_process
GO:0000122	negative regulation of tr anscription from RNA poly merase II promoter	IDA	biological_process
GO:0001666	response to hypoxia	IEA	biological_process
GO:0003677	DNA binding	IEA	molecular_function
GO:0003677	DNA binding	IEA	molecular_function
GO:0003682	chromatin binding	IEA	molecular_function
GO:0003714	transcription corepressor activity	IDA	molecular_function
GO:0003714	transcription corepressor activity	IMP	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	IEA	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	TAS	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	NAS	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	IDA	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005634	nucleus	IEA	cellular_component
GO:0005634	nucleus	IEA	cellular_component
GO:0005634	nucleus	IEA	cellular_component
GO:0005634	nucleus	TAS	cellular_component
GO:0005634	nucleus	IDA	cellular_component
GO:0005654	nucleoplasm	IDA	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0005737	cytoplasm	IEA	cellular_component
GO:0006306	DNA methylation	IEA	biological_process
GO:0006306	DNA methylation	TAS	biological_process
GO:0006306	DNA methylation	NAS	biological_process
GO:0006306	DNA methylation	NAS	biological_process
GO:0008168	methyltransferase activit y	IEA	molecular_function
GO:0008168	methyltransferase activit y	IEA	molecular_function
GO:0009008	DNA-methyltransferase act ivity	IEA	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	TAS	molecular_function
GO:0009636	response to toxic substan ce	IEA	biological_process
GO:0010212	response to ionizing radi ation	IEA	biological_process
GO:0010424	DNA methylation on cytosi ne within a CG sequence	IEA	biological_process
GO:0010468	regulation of gene expres sion	IEA	biological_process
GO:0010628	positive regulation of ge ne expression	IMP	biological_process
GO:0014823	response to activity	IEA	biological_process
GO:0016740	transferase activity	IEA	molecular_function
GO:0031000	response to caffeine	IEA	biological_process
GO:0032259	methylation	IEA	biological_process
GO:0032355	response to estradiol	IEA	biological_process
GO:0033189	response to vitamin A	IEA	biological_process
GO:0042220	response to cocaine	IEA	biological_process
GO:0042493	response to drug	IEA	biological_process
GO:0042826	histone deacetylase bindi ng	IEA	molecular_function
GO:0043231	intracellular membrane-bo unded organelle	IDA	cellular_component
GO:0045322	unmethylated CpG binding	IEA	molecular_function
GO:0045666	positive regulation of ne uron differentiation	IEA	biological_process
GO:0045814	negative regulation of ge ne expression, epigenetic	TAS	biological_process
GO:0045892	negative regulation of tr anscription, DNA-template d	IEA	biological_process
GO:0046498	S-adenosylhomocysteine me tabolic process	IEA	biological_process
GO:0046499	S-adenosylmethioninamine metabolic process	IEA	biological_process
GO:0046872	metal ion binding	IEA	molecular_function
GO:0051571	positive regulation of hi stone H3-K4 methylation	IMP	biological_process
GO:0051573	negative regulation of hi stone H3-K9 methylation	IMP	biological_process
GO:0051718	DNA (cytosine-5-)-methylt ransferase activity, acti ng on CpG substrates	IEA	molecular_function
GO:0071455	cellular response to hype roxia	IEA	biological_process
GO:0071549	cellular response to dexa methasone stimulus	IEA	biological_process
GO:0090116	C-5 methylation of cytosi ne	IEA	biological_process
GO:0000122	negative regulation of tr anscription from RNA poly merase II promoter	IDA	biological_process
GO:0003714	transcription corepressor activity	IDA	molecular_function
GO:0003714	transcription corepressor activity	IMP	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	TAS	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	NAS	molecular_function
GO:0003886	DNA (cytosine-5-)-methylt ransferase activity	IDA	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005634	nucleus	TAS	cellular_component
GO:0005634	nucleus	IDA	cellular_component
GO:0005654	nucleoplasm	IDA	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0006306	DNA methylation	TAS	biological_process
GO:0006306	DNA methylation	NAS	biological_process
GO:0006306	DNA methylation	NAS	biological_process
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	NAS	molecular_function
GO:0009008	DNA-methyltransferase act ivity	TAS	molecular_function
GO:0010628	positive regulation of ge ne expression	IMP	biological_process
GO:0043231	intracellular membrane-bo unded organelle	IDA	cellular_component
GO:0045814	negative regulation of ge ne expression, epigenetic	TAS	biological_process
GO:0051571	positive regulation of hi stone H3-K4 methylation	IMP	biological_process
GO:0051573	negative regulation of hi stone H3-K9 methylation	IMP	biological_process

KEGG pathways

hsa01100  Metabolic pathways
hsa05206  MicroRNAs in cancer
hsa00270  Cysteine and methionine metabolism

Diseases

Associated diseases	References
Cancer	PMID: 16211278
Endometrial cancer	PMID: 15661247
Endometriosis	PMID: 23888948
Humoral immunodeficiencies	KEGG: H00087
Male infertility	PMID: 17277043
Endometriosis	INFBASE22349384
Rheumatoid arthritis	PMID: 19777235
Spermatogenetic defects	PMID: 21482616

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes	Abstract
23888948	Endometrio sis					DNMT3B7 DNMT3B syncytin-1	Show abstract
22349384	Endometrio sis			40 (20 women wi th endometriosi s, the endometr ium in 20 women without endome triosis)		DNMT1 DNMT3a DNMT3b	Show abstract