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DNA (cytosine-5)-methyltransferase 3A (Dnmt3a) (EC 2.1.1.37) (DNA methyltransferase HsaIIIA) (DNA MTase HsaIIIA) (M.HsaIIIA)

 DNM3A_HUMAN             Reviewed;         912 AA.
Q9Y6K1; E9PEB8; Q86TE8; Q86XF5; Q8IZV0; Q8WXU9;
26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
15-JAN-2008, sequence version 4.
23-MAY-2018, entry version 167.
RecName: Full=DNA (cytosine-5)-methyltransferase 3A;
Short=Dnmt3a;
EC=2.1.1.37;
AltName: Full=DNA methyltransferase HsaIIIA;
Short=DNA MTase HsaIIIA;
Short=M.HsaIIIA;
Name=DNMT3A;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
TISSUE=Fetal testis;
PubMed=10433969; DOI=10.1016/S0378-1119(99)00252-8;
Xie S., Wang Z., Okano M., Nogami M., Li Y., He W.-W., Okumura K.,
Li E.;
"Cloning, expression and chromosome locations of the human DNMT3 gene
family.";
Gene 236:87-95(1999).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
PubMed=12138111; DOI=10.1074/jbc.M205312200;
Chen T., Ueda Y., Xie S., Li E.;
"A novel Dnmt3a isoform produced from an alternative promoter
localizes to euchromatin and its expression correlates with active de
novo methylation.";
J. Biol. Chem. 277:38746-38754(2002).
[3]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH DNMT1 AND
DNMT3B, AND SUBCELLULAR LOCATION.
PubMed=12145218; DOI=10.1093/emboj/cdf401;
Kim G.-D., Ni J., Kelesoglu N., Roberts R.J., Pradhan S.;
"Co-operation and communication between the human maintenance and de
novo DNA (cytosine-5) methyltransferases.";
EMBO J. 21:4183-4195(2002).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15815621; DOI=10.1038/nature03466;
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H.,
Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M.,
Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E.,
Kremitzki C., Oddy L., Du H., Sun H., Bradshaw-Cordum H., Ali J.,
Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C.,
Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J.,
Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A.,
Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K.,
Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M.,
Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N.,
Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M.,
Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E.,
Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P.,
Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A.,
Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A.,
Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T.,
Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D.,
Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X.,
McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
Miller W., Eichler E.E., Bork P., Suyama M., Torrents D.,
Waterston R.H., Wilson R.K.;
"Generation and annotation of the DNA sequences of human chromosomes 2
and 4.";
Nature 434:724-731(2005).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
TISSUE=Lung, PNS, and Skin;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[7]
TISSUE SPECIFICITY.
PubMed=10325416; DOI=10.1093/nar/27.11.2291;
Robertson K.D., Uzvolgyi E., Liang G., Talmadge C., Sumegi J.,
Gonzales F.A., Jones P.A.;
"The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate
mRNA expression in normal tissues and overexpression in tumors.";
Nucleic Acids Res. 27:2291-2298(1999).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,
Mann M.;
"Global, in vivo, and site-specific phosphorylation dynamics in
signaling networks.";
Cell 127:635-648(2006).
[9]
INTERACTION WITH SETDB1.
PubMed=16682412; DOI=10.1074/jbc.M513249200;
Li H., Rauch T., Chen Z.-X., Szabo P.E., Riggs A.D., Pfeifer G.P.;
"The histone methyltransferase SETDB1 and the DNA methyltransferase
DNMT3A interact directly and localize to promoters silenced in cancer
cells.";
J. Biol. Chem. 281:19489-19500(2006).
[10]
FUNCTION, AND INTERACTION WITH THE PRC2/EED-EZH2 COMPLEX.
PubMed=16357870; DOI=10.1038/nature04431;
Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C.,
Morey L., Van Eynde A., Bernard D., Vanderwinden J.-M., Bollen M.,
Esteller M., Di Croce L., de Launoit Y., Fuks F.;
"The Polycomb group protein EZH2 directly controls DNA methylation.";
Nature 439:871-874(2006).
[11]
ERRATUM.
Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C.,
Morey L., Van Eynde A., Bernard D., Vanderwinden J.-M., Bollen M.,
Esteller M., Di Croce L., de Launoit Y., Fuks F.;
Nature 446:824-824(2006).
[12]
DE NOVO DNA METHYLATION OF TARGET GENES.
PubMed=17200670; DOI=10.1038/ng1950;
Schlesinger Y., Straussman R., Keshet I., Farkash S., Hecht M.,
Zimmerman J., Eden E., Yakhini Z., Ben-Shushan E., Reubinoff B.E.,
Bergman Y., Simon I., Cedar H.;
"Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes
for de novo methylation in cancer.";
Nat. Genet. 39:232-236(2007).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[14]
INTERACTION WITH MPHOSPH8.
PubMed=20871592; DOI=10.1038/emboj.2010.239;
Kokura K., Sun L., Bedford M.T., Fang J.;
"Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing
and promotes tumour cell motility and invasion.";
EMBO J. 29:3673-3687(2010).
[15]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-243, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=20068231; DOI=10.1126/scisignal.2000475;
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
Mann M.;
"Quantitative phosphoproteomics reveals widespread full
phosphorylation site occupancy during mitosis.";
Sci. Signal. 3:RA3-RA3(2010).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105; SER-243; SER-255;
THR-261 AND SER-267, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[17]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma, and Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[18]
INVOLVEMENT IN TBRS, AND VARIANTS TBRS ASN-310; SER-532; LYS-548;
ARG-549; PRO-648; LEU-700; CYS-749; ASP-838; SER-902 AND LEU-904.
PubMed=24614070; DOI=10.1038/ng.2917;
Childhood Overgrowth Consortium;
Tatton-Brown K., Seal S., Ruark E., Harmer J., Ramsay E.,
Del Vecchio Duarte S., Zachariou A., Hanks S., O'Brien E.,
Aksglaede L., Baralle D., Dabir T., Gener B., Goudie D., Homfray T.,
Kumar A., Pilz D.T., Selicorni A., Temple I.K., Van Maldergem L.,
Yachelevich N., van Montfort R., Rahman N.;
"Mutations in the DNA methyltransferase gene DNMT3A cause an
overgrowth syndrome with intellectual disability.";
Nat. Genet. 46:385-388(2014).
[19]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-162, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=28112733; DOI=10.1038/nsmb.3366;
Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
Nielsen M.L.;
"Site-specific mapping of the human SUMO proteome reveals co-
modification with phosphorylation.";
Nat. Struct. Mol. Biol. 24:325-336(2017).
[20]
X-RAY CRYSTALLOGRAPHY (2.89 ANGSTROMS) OF 627-909 IN COMPLEX WITH
S-ADENOSYL-L-HOMOCYSTEINE, SUBUNIT, AND MUTAGENESIS OF PHE-732.
PubMed=17713477; DOI=10.1038/nature06146;
Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., Cheng X.;
"Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA
methylation.";
Nature 449:248-251(2007).
[21]
X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS) OF 476-614 IN COMPLEXES WITH
ZINC AND WITH HISTONE H3 PEPTIDE, AND SUBUNIT.
PubMed=19834512; DOI=10.1038/embor.2009.218;
Otani J., Nankumo T., Arita K., Inamoto S., Ariyoshi M., Shirakawa M.;
"Structural basis for recognition of H3K4 methylation status by the
DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.";
EMBO Rep. 10:1235-1241(2009).
[22]
X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) OF 40-53 IN COMPLEX WITH
MPHOSPH8, AND INTERACTION WITH MPHOSPH8.
PubMed=22086334; DOI=10.1038/ncomms1549;
Chang Y., Sun L., Kokura K., Horton J.R., Fukuda M., Espejo A.,
Izumi V., Koomen J.M., Bedford M.T., Zhang X., Shinkai Y., Fang J.,
Cheng X.;
"MPP8 mediates the interactions between DNA methyltransferase Dnmt3a
and H3K9 methyltransferase GLP/G9a.";
Nat. Commun. 2:533-533(2011).
[23]
X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 275-427.
PubMed=21720545; DOI=10.1371/journal.pone.0018919;
Wu H., Zeng H., Lam R., Tempel W., Amaya M.F., Xu C., Dombrovski L.,
Qiu W., Wang Y., Min J.;
"Structural and histone binding ability characterizations of human
PWWP domains.";
PLoS ONE 6:E18919-E18919(2011).
[24]
VARIANTS ASP-699; PHE-731 DEL; CYS-882; HIS-882 AND PRO-882.
PubMed=21828135; DOI=10.1182/blood-2010-10-311019;
Jankowska A.M., Makishima H., Tiu R.V., Szpurka H., Huang Y.,
Traina F., Visconte V., Sugimoto Y., Prince C., O'Keefe C., Hsi E.D.,
List A., Sekeres M.A., Rao A., McDevitt M.A., Maciejewski J.P.;
"Mutational spectrum analysis of chronic myelomonocytic leukemia
includes genes associated with epigenetic regulation: UTX, EZH2, and
DNMT3A.";
Blood 118:3932-3941(2011).
[25]
VARIANT TBRS GLN-771.
PubMed=27701732; DOI=10.1111/cge.12878;
Xin B., Cruz Marino T., Szekely J., Leblanc J., Cechner K., Sency V.,
Wensel C., Barabas M., Therriault V., Wang H.;
"Novel DNMT3A germline mutations are associated with inherited Tatton-
Brown-Rahman syndrome.";
Clin. Genet. 91:623-628(2017).
[26]
VARIANTS TBRS CYS-365; ASN-529; GLY-778 AND CYS-882.
PubMed=27317772; DOI=10.1136/jmedgenet-2015-103638;
Tlemsani C., Luscan A., Leulliot N., Bieth E., Afenjar A., Baujat G.,
Doco-Fenzy M., Goldenberg A., Lacombe D., Lambert L., Odent S.,
Pasche J., Sigaudy S., Buffet A., Violle-Poirsier C.,
Briand-Suleau A., Laurendeau I., Chin M., Saugier-Veber P., Vidaud D.,
Cormier-Daire V., Vidaud M., Pasmant E., Burglen L.;
"SETD2 and DNMT3A screen in the Sotos-like syndrome French cohort.";
J. Med. Genet. 0:0-0(2016).
-!- FUNCTION: Required for genome-wide de novo methylation and is
essential for the establishment of DNA methylation patterns during
development. DNA methylation is coordinated with methylation of
histones. It modifies DNA in a non-processive manner and also
methylates non-CpG sites. May preferentially methylate DNA linker
between 2 nucleosomal cores and is inhibited by histone H1. Plays
a role in paternal and maternal imprinting. Required for
methylation of most imprinted loci in germ cells. Acts as a
transcriptional corepressor for ZBTB18. Recruited to trimethylated
'Lys-36' of histone H3 (H3K36me3) sites. Can actively repress
transcription through the recruitment of HDAC activity.
{ECO:0000269|PubMed:16357870}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + DNA = S-adenosyl-L-
homocysteine + DNA containing 5-methylcytosine.
{ECO:0000255|PROSITE-ProRule:PRU10018}.
-!- ENZYME REGULATION: Activated by binding to the regulatory factor
DNMT3L. {ECO:0000250}.
-!- SUBUNIT: Heterotetramer composed of 1 DNMT3A homodimer and 2
DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with
UBC9, PIAS1 and PIAS2 (By similarity). Binds the ZBTB18
transcriptional repressor. Interacts with SETDB1. Associates with
HDAC1 through its ADD domain. Interacts with UHRF1 (By
similarity). Interacts with DNMT1 and DNMT3B. Interacts with the
PRC2/EED-EZH2 complex. Interacts with MPHOSPH8. Interacts with
histone H3 that is not methylated at 'Lys-4' (H3K4). {ECO:0000250,
ECO:0000269|PubMed:12145218, ECO:0000269|PubMed:16357870,
ECO:0000269|PubMed:16682412, ECO:0000269|PubMed:17713477,
ECO:0000269|PubMed:19834512, ECO:0000269|PubMed:20871592,
ECO:0000269|PubMed:22086334}.
-!- INTERACTION:
Self; NbExp=4; IntAct=EBI-923653, EBI-923653;
Q03060:CREM; NbExp=2; IntAct=EBI-923653, EBI-3907794;
Q9UJW3-1:DNMT3L; NbExp=5; IntAct=EBI-923653, EBI-15650345;
O75530:EED; NbExp=2; IntAct=EBI-923653, EBI-923794;
Q15910:EZH2; NbExp=6; IntAct=EBI-923653, EBI-530054;
P84243:H3F3B; NbExp=7; IntAct=EBI-923653, EBI-120658;
Q99750:MDFI; NbExp=4; IntAct=EBI-923653, EBI-724076;
Q9QR71:ORF73 (xeno); NbExp=3; IntAct=EBI-923653, EBI-15602554;
O14744:PRMT5; NbExp=4; IntAct=EBI-923653, EBI-351098;
Q15047:SETDB1; NbExp=7; IntAct=EBI-923653, EBI-79691;
P23497:SP100; NbExp=3; IntAct=EBI-923653, EBI-751145;
P56279:TCL1A; NbExp=5; IntAct=EBI-923653, EBI-749995;
Q96T88:UHRF1; NbExp=7; IntAct=EBI-923653, EBI-1548946;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12145218}.
Cytoplasm {ECO:0000269|PubMed:12145218}. Note=Accumulates in the
major satellite repeats at pericentric heterochromatin.
{ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative promoter usage, Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q9Y6K1-1; Sequence=Displayed;
Name=2;
IsoId=Q9Y6K1-2; Sequence=VSP_046254;
Note=It is uncertain whether Met-1 or Met-35 is the initiator.;
Name=3;
IsoId=Q9Y6K1-3; Sequence=VSP_040998, VSP_040999;
Note=Produced by alternative splicing.;
-!- TISSUE SPECIFICITY: Highly expressed in fetal tissues, skeletal
muscle, heart, peripheral blood mononuclear cells, kidney, and at
lower levels in placenta, brain, liver, colon, spleen, small
intestine and lung. {ECO:0000269|PubMed:10325416}.
-!- DOMAIN: The PWWP domain is essential for targeting to pericentric
heterochromatin. It specifically recognizes and binds
trimethylated 'Lys-36' of histone H3 (H3K36me3) (By similarity).
{ECO:0000250}.
-!- PTM: Sumoylated; sumoylation disrupts the ability to interact with
histone deacetylases (HDAC1 and HDAC2) and repress transcription.
{ECO:0000250}.
-!- DISEASE: Tatton-Brown-Rahman syndrome (TBRS) [MIM:615879]: An
overgrowth syndrome characterized by a distinctive facial
appearance, tall stature and intellectual disability. Facial
gestalt is characterized by a round face, heavy horizontal
eyebrows and narrow palpebral fissures. Less common features
include atrial septal defects, seizures, umbilical hernia, and
scoliosis. {ECO:0000269|PubMed:24614070,
ECO:0000269|PubMed:27317772, ECO:0000269|PubMed:27701732}.
Note=The disease is caused by mutations affecting the gene
represented in this entry.
-!- SIMILARITY: Belongs to the class I-like SAM-binding
methyltransferase superfamily. C5-methyltransferase family.
{ECO:0000255|PROSITE-ProRule:PRU01016}.
-!- CAUTION: It is uncertain whether Met-1 or Met-4 is the initiator.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAL57039.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=AAN40037.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
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EMBL; AF067972; AAD33084.2; -; mRNA.
EMBL; AF480163; AAN40037.1; ALT_INIT; mRNA.
EMBL; AF331856; AAL57039.1; ALT_INIT; mRNA.
EMBL; AC012074; AAY14761.1; -; Genomic_DNA.
EMBL; CH471053; EAX00727.1; -; Genomic_DNA.
EMBL; BC032392; AAH32392.1; -; mRNA.
EMBL; BC043617; AAH43617.1; -; mRNA.
EMBL; BC051864; AAH51864.1; -; mRNA.
CCDS; CCDS1718.2; -. [Q9Y6K1-2]
CCDS; CCDS33157.1; -. [Q9Y6K1-1]
CCDS; CCDS46232.1; -. [Q9Y6K1-3]
RefSeq; NP_001307821.1; NM_001320892.1. [Q9Y6K1-3]
RefSeq; NP_001307822.1; NM_001320893.1.
RefSeq; NP_072046.2; NM_022552.4. [Q9Y6K1-1]
RefSeq; NP_715640.2; NM_153759.3. [Q9Y6K1-2]
RefSeq; NP_783328.1; NM_175629.2. [Q9Y6K1-1]
RefSeq; NP_783329.1; NM_175630.1. [Q9Y6K1-3]
RefSeq; XP_005264232.1; XM_005264175.4. [Q9Y6K1-1]
RefSeq; XP_005264234.1; XM_005264177.4.
RefSeq; XP_011530969.1; XM_011532667.2.
RefSeq; XP_016859015.1; XM_017003526.1. [Q9Y6K1-1]
RefSeq; XP_016859016.1; XM_017003527.1.
UniGene; Hs.515840; -.
PDB; 2QRV; X-ray; 2.89 A; A/D/E/H=627-912.
PDB; 3A1A; X-ray; 2.30 A; A=476-614.
PDB; 3A1B; X-ray; 2.29 A; A=476-614.
PDB; 3LLR; X-ray; 2.30 A; A/B/C/D/E=275-427.
PDB; 3SVM; X-ray; 2.31 A; P=40-53.
PDB; 4QBQ; X-ray; 2.41 A; A/C=479-610.
PDB; 4QBR; X-ray; 1.90 A; A/C=476-611.
PDB; 4QBS; X-ray; 1.80 A; A=476-611.
PDB; 4U7P; X-ray; 3.82 A; A=455-912.
PDB; 4U7T; X-ray; 2.90 A; A/C=476-912.
PDB; 5YX2; X-ray; 2.65 A; A/D=628-912.
PDB; 6BRR; X-ray; 2.97 A; A/D=628-912.
PDB; 6F57; X-ray; 3.10 A; A/D=628-912.
PDBsum; 2QRV; -.
PDBsum; 3A1A; -.
PDBsum; 3A1B; -.
PDBsum; 3LLR; -.
PDBsum; 3SVM; -.
PDBsum; 4QBQ; -.
PDBsum; 4QBR; -.
PDBsum; 4QBS; -.
PDBsum; 4U7P; -.
PDBsum; 4U7T; -.
PDBsum; 5YX2; -.
PDBsum; 6BRR; -.
PDBsum; 6F57; -.
ProteinModelPortal; Q9Y6K1; -.
SMR; Q9Y6K1; -.
BioGrid; 108125; 54.
CORUM; Q9Y6K1; -.
DIP; DIP-38004N; -.
IntAct; Q9Y6K1; 31.
MINT; Q9Y6K1; -.
STRING; 9606.ENSP00000264709; -.
BindingDB; Q9Y6K1; -.
ChEMBL; CHEMBL1992; -.
REBASE; 4119; M.HsaDnmt3A.
iPTMnet; Q9Y6K1; -.
PhosphoSitePlus; Q9Y6K1; -.
BioMuta; DNMT3A; -.
DMDM; 166215081; -.
EPD; Q9Y6K1; -.
PaxDb; Q9Y6K1; -.
PeptideAtlas; Q9Y6K1; -.
PRIDE; Q9Y6K1; -.
DNASU; 1788; -.
Ensembl; ENST00000264709; ENSP00000264709; ENSG00000119772. [Q9Y6K1-1]
Ensembl; ENST00000321117; ENSP00000324375; ENSG00000119772. [Q9Y6K1-1]
Ensembl; ENST00000380746; ENSP00000370122; ENSG00000119772. [Q9Y6K1-2]
Ensembl; ENST00000406659; ENSP00000384852; ENSG00000119772. [Q9Y6K1-3]
GeneID; 1788; -.
KEGG; hsa:1788; -.
UCSC; uc002rgb.5; human. [Q9Y6K1-1]
CTD; 1788; -.
DisGeNET; 1788; -.
EuPathDB; HostDB:ENSG00000119772.16; -.
GeneCards; DNMT3A; -.
HGNC; HGNC:2978; DNMT3A.
HPA; CAB009469; -.
HPA; HPA026588; -.
MalaCards; DNMT3A; -.
MIM; 602769; gene.
MIM; 615879; phenotype.
neXtProt; NX_Q9Y6K1; -.
OpenTargets; ENSG00000119772; -.
Orphanet; 404443; Tall stature-intellectual disability-facial dysmorphism syndrome.
PharmGKB; PA27445; -.
eggNOG; ENOG410IGHW; Eukaryota.
eggNOG; ENOG410XQ4Y; LUCA.
GeneTree; ENSGT00390000008341; -.
HOGENOM; HOG000230875; -.
HOVERGEN; HBG051381; -.
InParanoid; Q9Y6K1; -.
KO; K17398; -.
OMA; FPVCHDS; -.
OrthoDB; EOG091G01TP; -.
PhylomeDB; Q9Y6K1; -.
TreeFam; TF329039; -.
BRENDA; 2.1.1.37; 2681.
Reactome; R-HSA-212300; PRC2 methylates histones and DNA.
Reactome; R-HSA-3214858; RMTs methylate histone arginines.
Reactome; R-HSA-5334118; DNA methylation.
SIGNOR; Q9Y6K1; -.
ChiTaRS; DNMT3A; human.
EvolutionaryTrace; Q9Y6K1; -.
GenomeRNAi; 1788; -.
PRO; PR:Q9Y6K1; -.
Proteomes; UP000005640; Chromosome 2.
Bgee; ENSG00000119772; -.
CleanEx; HS_DNMT3A; -.
ExpressionAtlas; Q9Y6K1; baseline and differential.
Genevisible; Q9Y6K1; HS.
GO; GO:0000775; C:chromosome, centromeric region; IEA:Ensembl.
GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
GO; GO:0000791; C:euchromatin; IDA:UniProtKB.
GO; GO:0005720; C:nuclear heterochromatin; IEA:Ensembl.
GO; GO:0016363; C:nuclear matrix; IDA:UniProtKB.
GO; GO:0005654; C:nucleoplasm; IDA:HPA.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0001741; C:XY body; IEA:Ensembl.
GO; GO:0003682; F:chromatin binding; IEA:Ensembl.
GO; GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
GO; GO:0009008; F:DNA-methyltransferase activity; TAS:Reactome.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000981; F:RNA polymerase II transcription factor activity, sequence-specific DNA binding; ISA:NTNU_SB.
GO; GO:0007568; P:aging; IEA:Ensembl.
GO; GO:0071230; P:cellular response to amino acid stimulus; IEA:Ensembl.
GO; GO:0071361; P:cellular response to ethanol; IEA:Ensembl.
GO; GO:0071456; P:cellular response to hypoxia; IEA:Ensembl.
GO; GO:0006306; P:DNA methylation; IDA:UniProtKB.
GO; GO:0043045; P:DNA methylation involved in embryo development; IEA:Ensembl.
GO; GO:0043046; P:DNA methylation involved in gamete generation; IEA:Ensembl.
GO; GO:0097284; P:hepatocyte apoptotic process; IEA:Ensembl.
GO; GO:0006346; P:methylation-dependent chromatin silencing; IEA:Ensembl.
GO; GO:0000278; P:mitotic cell cycle; IEA:Ensembl.
GO; GO:0045814; P:negative regulation of gene expression, epigenetic; TAS:Reactome.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IEA:Ensembl.
GO; GO:0030182; P:neuron differentiation; IEA:Ensembl.
GO; GO:0010942; P:positive regulation of cell death; IEA:Ensembl.
GO; GO:0006349; P:regulation of gene expression by genetic imprinting; TAS:UniProtKB.
GO; GO:0042220; P:response to cocaine; IEA:Ensembl.
GO; GO:0032355; P:response to estradiol; IEA:Ensembl.
GO; GO:0010212; P:response to ionizing radiation; IEA:Ensembl.
GO; GO:0010288; P:response to lead ion; IEA:Ensembl.
GO; GO:0033189; P:response to vitamin A; IEA:Ensembl.
GO; GO:0007283; P:spermatogenesis; IEA:Ensembl.
InterPro; IPR025766; ADD.
InterPro; IPR018117; C5_DNA_meth_AS.
InterPro; IPR001525; C5_MeTfrase.
InterPro; IPR030487; DNMT3A.
InterPro; IPR000313; PWWP_dom.
InterPro; IPR029063; SAM-dependent_MTases.
PANTHER; PTHR23068:SF10; PTHR23068:SF10; 2.
Pfam; PF00145; DNA_methylase; 1.
Pfam; PF00855; PWWP; 1.
SMART; SM00293; PWWP; 1.
SUPFAM; SSF53335; SSF53335; 1.
PROSITE; PS51533; ADD; 1.
PROSITE; PS00094; C5_MTASE_1; 1.
PROSITE; PS50812; PWWP; 1.
PROSITE; PS51679; SAM_MT_C5; 1.
1: Evidence at protein level;
3D-structure; Alternative promoter usage; Alternative splicing;
Chromatin regulator; Complete proteome; Cytoplasm; Disease mutation;
DNA-binding; Isopeptide bond; Mental retardation; Metal-binding;
Methylation; Methyltransferase; Nucleus; Phosphoprotein; Polymorphism;
Reference proteome; Repressor; S-adenosyl-L-methionine; Transferase;
Ubl conjugation; Zinc; Zinc-finger.
CHAIN 1 912 DNA (cytosine-5)-methyltransferase 3A.
/FTId=PRO_0000088043.
DOMAIN 292 350 PWWP. {ECO:0000255|PROSITE-
ProRule:PRU00162}.
DOMAIN 482 614 ADD. {ECO:0000255|PROSITE-
ProRule:PRU00865}.
DOMAIN 634 912 SAM-dependent MTase C5-type.
{ECO:0000255|PROSITE-ProRule:PRU01016}.
ZN_FING 493 523 GATA-type; atypical.
{ECO:0000255|PROSITE-ProRule:PRU00865}.
ZN_FING 534 590 PHD-type; atypical. {ECO:0000255|PROSITE-
ProRule:PRU00865}.
REGION 199 403 Interaction with DNMT1 and DNMT3B.
{ECO:0000269|PubMed:12145218}.
REGION 494 586 Interaction with the PRC2/EED-EZH2
complex. {ECO:0000250}.
REGION 641 645 S-adenosyl-L-methionine binding.
{ECO:0000244|PDB:2QRV,
ECO:0000269|PubMed:17713477}.
REGION 686 688 S-adenosyl-L-methionine binding.
{ECO:0000244|PDB:2QRV,
ECO:0000269|PubMed:17713477}.
REGION 891 893 S-adenosyl-L-methionine binding.
{ECO:0000244|PDB:2QRV,
ECO:0000269|PubMed:17713477}.
ACT_SITE 710 710 {ECO:0000255|PROSITE-ProRule:PRU01016,
ECO:0000255|PROSITE-ProRule:PRU10018}.
BINDING 664 664 S-adenosyl-L-methionine.
{ECO:0000244|PDB:2QRV,
ECO:0000269|PubMed:17713477}.
MOD_RES 105 105 Phosphoserine.
{ECO:0000244|PubMed:17081983,
ECO:0000244|PubMed:18669648,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163}.
MOD_RES 124 124 Phosphothreonine.
{ECO:0000250|UniProtKB:Q1LZ53}.
MOD_RES 171 171 Omega-N-methylarginine.
{ECO:0000250|UniProtKB:O88508}.
MOD_RES 243 243 Phosphoserine.
{ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692}.
MOD_RES 255 255 Phosphoserine.
{ECO:0000244|PubMed:21406692}.
MOD_RES 261 261 Phosphothreonine.
{ECO:0000244|PubMed:21406692}.
MOD_RES 267 267 Phosphoserine.
{ECO:0000244|PubMed:21406692}.
MOD_RES 390 390 Phosphoserine.
{ECO:0000250|UniProtKB:O88508}.
MOD_RES 393 393 Phosphoserine.
{ECO:0000250|UniProtKB:O88508}.
CROSSLNK 162 162 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
VAR_SEQ 1 213 MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEP
STTARKVGRPGRKRKHPPVESGDTPKDPAVISKSPSMAQDS
GASELLPNGDLEKRSEPQPEEGSPAGGQKGGAPAEGEGAAE
TLPEASRAVENGCCTPKEGRGAPAEAGKEQKETNIESMKME
GSRGRLRGGLGWESSLRQRPMPRLTFQAGDPYYISKRKRDE
WLARWKRE -> MGILERVVRRNGRVDRSLKDECDT (in
isoform 2).
{ECO:0000303|PubMed:12138111}.
/FTId=VSP_046254.
VAR_SEQ 151 166 KEQKETNIESMKMEGS -> ESSAPGAASSGPTSIP (in
isoform 3).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_040998.
VAR_SEQ 167 912 Missing (in isoform 3).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_040999.
VARIANT 310 310 I -> N (in TBRS; somatic mutation;
dbSNP:rs587777508).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071463.
VARIANT 365 365 Y -> C (in TBRS; unknown pathological
significance; dbSNP:rs144062658).
{ECO:0000269|PubMed:27317772}.
/FTId=VAR_077522.
VARIANT 529 529 D -> N (in TBRS; unknown pathological
significance; dbSNP:rs962805778).
{ECO:0000269|PubMed:27317772}.
/FTId=VAR_077523.
VARIANT 532 532 G -> S (in TBRS; somatic mutation;
dbSNP:rs951361433).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071464.
VARIANT 548 548 M -> K (in TBRS; somatic mutation;
dbSNP:rs587777509).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071465.
VARIANT 549 549 C -> R (in TBRS; somatic mutation).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071466.
VARIANT 648 648 L -> P (in TBRS; somatic mutation;
dbSNP:rs587777507).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071467.
VARIANT 699 699 G -> D (in a patient with chronic
myelomonocytic leukemia;
dbSNP:rs761064473).
{ECO:0000269|PubMed:21828135}.
/FTId=VAR_067234.
VARIANT 700 700 P -> L (in TBRS; somatic mutation;
dbSNP:rs772368909).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071468.
VARIANT 731 731 Missing (in a patient with chronic
myelomonocytic leukemia).
{ECO:0000269|PubMed:21828135}.
/FTId=VAR_067235.
VARIANT 749 749 R -> C (in TBRS; somatic mutation;
dbSNP:rs754613602).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071469.
VARIANT 771 771 R -> Q (in TBRS; unknown pathological
significance; dbSNP:rs757823678).
{ECO:0000269|PubMed:27701732}.
/FTId=VAR_077524.
VARIANT 778 778 V -> G (in TBRS; unknown pathological
significance; dbSNP:rs979932565).
{ECO:0000269|PubMed:27317772}.
/FTId=VAR_077525.
VARIANT 838 838 N -> D (in TBRS; somatic mutation;
dbSNP:rs961377711).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071470.
VARIANT 882 882 R -> C (in a patient with chronic
myelomonocytic leukemia; somatic
mutation; dbSNP:rs377577594).
{ECO:0000269|PubMed:21828135}.
/FTId=VAR_067236.
VARIANT 882 882 R -> H (in a patient with chronic
myelomonocytic leukemia; somatic
mutation; dbSNP:rs147001633).
{ECO:0000269|PubMed:21828135}.
/FTId=VAR_067237.
VARIANT 882 882 R -> P (in a patient with chronic
myelomonocytic leukemia; somatic
mutation; dbSNP:rs147001633).
{ECO:0000269|PubMed:21828135}.
/FTId=VAR_067238.
VARIANT 902 902 F -> S (in TBRS; somatic mutation;
dbSNP:rs587777510).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071471.
VARIANT 904 904 P -> L (in TBRS; somatic mutation;
dbSNP:rs149095705).
{ECO:0000269|PubMed:24614070}.
/FTId=VAR_071472.
MUTAGEN 732 732 F->A: Loss of activity du to the
incapacity to bind the regulatory subunit
DNMT3L. {ECO:0000269|PubMed:17713477}.
STRAND 295 298 {ECO:0000244|PDB:3LLR}.
STRAND 306 311 {ECO:0000244|PDB:3LLR}.
HELIX 313 315 {ECO:0000244|PDB:3LLR}.
STRAND 325 330 {ECO:0000244|PDB:3LLR}.
TURN 331 333 {ECO:0000244|PDB:3LLR}.
STRAND 336 340 {ECO:0000244|PDB:3LLR}.
HELIX 341 343 {ECO:0000244|PDB:3LLR}.
STRAND 344 346 {ECO:0000244|PDB:3LLR}.
HELIX 347 349 {ECO:0000244|PDB:3LLR}.
HELIX 350 353 {ECO:0000244|PDB:3LLR}.
HELIX 356 361 {ECO:0000244|PDB:3LLR}.
HELIX 363 380 {ECO:0000244|PDB:3LLR}.
HELIX 393 395 {ECO:0000244|PDB:3LLR}.
HELIX 399 411 {ECO:0000244|PDB:3LLR}.
TURN 415 417 {ECO:0000244|PDB:3LLR}.
HELIX 419 422 {ECO:0000244|PDB:3LLR}.
HELIX 476 484 {ECO:0000244|PDB:4QBS}.
HELIX 490 492 {ECO:0000244|PDB:4QBS}.
TURN 495 497 {ECO:0000244|PDB:4QBS}.
STRAND 502 505 {ECO:0000244|PDB:4QBS}.
STRAND 507 514 {ECO:0000244|PDB:4QBS}.
HELIX 515 524 {ECO:0000244|PDB:4QBS}.
STRAND 532 536 {ECO:0000244|PDB:4QBS}.
TURN 538 540 {ECO:0000244|PDB:4QBS}.
STRAND 544 548 {ECO:0000244|PDB:4QBS}.
TURN 552 554 {ECO:0000244|PDB:4QBR}.
STRAND 557 559 {ECO:0000244|PDB:4QBS}.
HELIX 560 566 {ECO:0000244|PDB:4QBS}.
HELIX 571 577 {ECO:0000244|PDB:4QBS}.
STRAND 578 580 {ECO:0000244|PDB:4QBS}.
TURN 584 586 {ECO:0000244|PDB:4QBS}.
STRAND 587 589 {ECO:0000244|PDB:4QBQ}.
STRAND 595 597 {ECO:0000244|PDB:4QBS}.
HELIX 601 608 {ECO:0000244|PDB:4QBS}.
HELIX 628 630 {ECO:0000244|PDB:4U7T}.
STRAND 634 639 {ECO:0000244|PDB:5YX2}.
TURN 642 644 {ECO:0000244|PDB:5YX2}.
HELIX 645 652 {ECO:0000244|PDB:5YX2}.
STRAND 657 663 {ECO:0000244|PDB:5YX2}.
HELIX 667 676 {ECO:0000244|PDB:5YX2}.
TURN 677 679 {ECO:0000244|PDB:5YX2}.
STRAND 681 683 {ECO:0000244|PDB:5YX2}.
HELIX 687 689 {ECO:0000244|PDB:5YX2}.
HELIX 692 698 {ECO:0000244|PDB:5YX2}.
STRAND 702 706 {ECO:0000244|PDB:5YX2}.
TURN 711 713 {ECO:0000244|PDB:5YX2}.
TURN 722 724 {ECO:0000244|PDB:2QRV}.
HELIX 728 730 {ECO:0000244|PDB:5YX2}.
HELIX 731 741 {ECO:0000244|PDB:5YX2}.
STRAND 752 761 {ECO:0000244|PDB:5YX2}.
HELIX 763 773 {ECO:0000244|PDB:5YX2}.
STRAND 778 781 {ECO:0000244|PDB:5YX2}.
HELIX 782 784 {ECO:0000244|PDB:5YX2}.
STRAND 786 788 {ECO:0000244|PDB:5YX2}.
STRAND 791 796 {ECO:0000244|PDB:5YX2}.
TURN 799 802 {ECO:0000244|PDB:5YX2}.
HELIX 815 818 {ECO:0000244|PDB:5YX2}.
STRAND 824 826 {ECO:0000244|PDB:5YX2}.
STRAND 828 830 {ECO:0000244|PDB:5YX2}.
HELIX 837 840 {ECO:0000244|PDB:5YX2}.
TURN 843 846 {ECO:0000244|PDB:5YX2}.
STRAND 849 852 {ECO:0000244|PDB:5YX2}.
STRAND 855 857 {ECO:0000244|PDB:5YX2}.
HELIX 861 868 {ECO:0000244|PDB:5YX2}.
TURN 872 875 {ECO:0000244|PDB:2QRV}.
HELIX 882 891 {ECO:0000244|PDB:5YX2}.
HELIX 895 902 {ECO:0000244|PDB:5YX2}.
HELIX 903 905 {ECO:0000244|PDB:5YX2}.
TURN 906 908 {ECO:0000244|PDB:5YX2}.
SEQUENCE 912 AA; 101858 MW; BD1FF7C5B4F54A33 CRC64;
MPAMPSSGPG DTSSSAAERE EDRKDGEEQE EPRGKEERQE PSTTARKVGR PGRKRKHPPV
ESGDTPKDPA VISKSPSMAQ DSGASELLPN GDLEKRSEPQ PEEGSPAGGQ KGGAPAEGEG
AAETLPEASR AVENGCCTPK EGRGAPAEAG KEQKETNIES MKMEGSRGRL RGGLGWESSL
RQRPMPRLTF QAGDPYYISK RKRDEWLARW KREAEKKAKV IAGMNAVEEN QGPGESQKVE
EASPPAVQQP TDPASPTVAT TPEPVGSDAG DKNATKAGDD EPEYEDGRGF GIGELVWGKL
RGFSWWPGRI VSWWMTGRSR AAEGTRWVMW FGDGKFSVVC VEKLMPLSSF CSAFHQATYN
KQPMYRKAIY EVLQVASSRA GKLFPVCHDS DESDTAKAVE VQNKPMIEWA LGGFQPSGPK
GLEPPEEEKN PYKEVYTDMW VEPEAAAYAP PPPAKKPRKS TAEKPKVKEI IDERTRERLV
YEVRQKCRNI EDICISCGSL NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC
CGGREVLMCG NNNCCRCFCV ECVDLLVGPG AAQAAIKEDP WNCYMCGHKG TYGLLRRRED
WPSRLQMFFA NNHDQEFDPP KVYPPVPAEK RKPIRVLSLF DGIATGLLVL KDLGIQVDRY
IASEVCEDSI TVGMVRHQGK IMYVGDVRSV TQKHIQEWGP FDLVIGGSPC NDLSIVNPAR
KGLYEGTGRL FFEFYRLLHD ARPKEGDDRP FFWLFENVVA MGVSDKRDIS RFLESNPVMI
DAKEVSAAHR ARYFWGNLPG MNRPLASTVN DKLELQECLE HGRIAKFSKV RTITTRSNSI
KQGKDQHFPV FMNEKEDILW CTEMERVFGF PVHYTDVSNM SRLARQRLLG RSWSVPVIRH
LFAPLKEYFA CV


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