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Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5 (EC 2.1.1.43) (Histone H3-K9 methyltransferase dim-5) (H3-K9-HMTase dim-5) (HKMT)

 DIM5_NEUCR              Reviewed;         331 AA.
Q8X225; Q1K5Y7;
01-FEB-2005, integrated into UniProtKB/Swiss-Prot.
04-DEC-2007, sequence version 2.
22-APR-2020, entry version 117.
RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5;
EC=2.1.1.355 {ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12679815, ECO:0000269|PubMed:12887903};
AltName: Full=Histone H3-K9 methyltransferase dim-5;
Short=H3-K9-HMTase dim-5;
Short=HKMT;
Name=dim-5; ORFNames=29E8.110, NCU04402;
Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 /
FGSC 987).
Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes;
Sordariomycetidae; Sordariales; Sordariaceae; Neurospora.
NCBI_TaxID=367110;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
STRAIN=ATCC 18889 / 74-OR8-1a / 40-21 / DSM 1258 / FGSC 988;
PubMed=11713521; DOI=10.1038/35104508;
Tamaru H., Selker E.U.;
"A histone H3 methyltransferase controls DNA methylation in Neurospora
crassa.";
Nature 414:277-283(2001).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987;
PubMed=12655011; DOI=10.1093/nar/gkg293;
Mannhaupt G., Montrone C., Haase D., Mewes H.-W., Aign V., Hoheisel J.D.,
Fartmann B., Nyakatura G., Kempken F., Maier J., Schulte U.;
"What's in the genome of a filamentous fungus? Analysis of the Neurospora
genome sequence.";
Nucleic Acids Res. 31:1944-1954(2003).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987;
PubMed=12712197; DOI=10.1038/nature01554;
Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D.,
Jaffe D.B., FitzHugh W., Ma L.-J., Smirnov S., Purcell S., Rehman B.,
Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M.,
Qui D., Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M.,
Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U.,
Kothe G.O., Jedd G., Mewes H.-W., Staben C., Marcotte E., Greenberg D.,
Roy A., Foley K., Naylor J., Stange-Thomann N., Barrett R., Gnerre S.,
Kamal M., Kamvysselis M., Mauceli E.W., Bielke C., Rudd S., Frishman D.,
Krystofova S., Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S.,
Cogoni C., Macino G., Catcheside D.E.A., Li W., Pratt R.J., Osmani S.A.,
DeSouza C.P.C., Glass N.L., Orbach M.J., Berglund J.A., Voelker R.,
Yarden O., Plamann M., Seiler S., Dunlap J.C., Radford A., Aramayo R.,
Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I.,
Sachs M.S., Lander E.S., Nusbaum C., Birren B.W.;
"The genome sequence of the filamentous fungus Neurospora crassa.";
Nature 422:859-868(2003).
[4]
FUNCTION, CATALYTIC ACTIVITY, AND METHYLATION OF HISTONE H3.
PubMed=12679815; DOI=10.1038/ng1143;
Tamaru H., Zhang X., McMillen D., Singh P.B., Nakayama J., Grewal S.I.,
Allis C.D., Cheng X., Selker E.U.;
"Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in
Neurospora crassa.";
Nat. Genet. 34:75-79(2003).
[5]
SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF PHE-281.
PubMed=15590646; DOI=10.1074/jbc.m410483200;
Collins R.E., Tachibana M., Tamaru H., Smith K.M., Jia D., Zhang X.,
Selker E.U., Shinkai Y., Cheng X.;
"In vitro and in vivo analyses of a Phe/Tyr switch controlling product
specificity of histone lysine methyltransferases.";
J. Biol. Chem. 280:5563-5570(2005).
[6]
SUBSTRATE SPECIFICITY.
PubMed=18215768; DOI=10.1016/j.chembiol.2007.11.013;
Rathert P., Zhang X., Freund C., Cheng X., Jeltsch A.;
"Analysis of the substrate specificity of the Dim-5 histone lysine
methyltransferase using peptide arrays.";
Chem. Biol. 15:5-11(2008).
[7]
X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF 30-331 IN COMPLEX WITH ZINC IONS,
FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ARG-251; ASN-254; HIS-255
AND TYR-296.
PubMed=12372305; DOI=10.1016/s0092-8674(02)00999-6;
Zhang X., Tamaru H., Khan S.I., Horton J.R., Keefe L.J., Selker E.U.,
Cheng X.;
"Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine
methyltransferase.";
Cell 111:117-127(2002).
[8]
X-RAY CRYSTALLOGRAPHY (2.59 ANGSTROMS) OF 30-331 IN COMPLEX WITH HISTONE
H3; S-ADENOSYL-L-HOMOCYSTEINE AND ZINC IONS, FUNCTION, CATALYTIC ACTIVITY,
AND MUTAGENESIS OF TYR-191; ASP-222; PHE-294; LEU-330 AND TRP-331.
PubMed=12887903; DOI=10.1016/s1097-2765(03)00224-7;
Zhang X., Yang Z., Khan S.I., Horton J.R., Tamaru H., Selker E.U.,
Cheng X.;
"Structural basis for the product specificity of histone lysine
methyltransferases.";
Mol. Cell 12:177-185(2003).
-!- FUNCTION: Histone methyltransferase that specifically trimethylates
histone H3 to form H3K9me3. H3K9me3 marks chromatin regions for DNA
methylation (PubMed:11713521, PubMed:12372305, PubMed:12679815,
PubMed:12887903). Dim-5 recognizes Arg-8 to Gly-12 of the H3 tail with
Thr-11 and Gly-12 being the most important specificity determinants,
the recognition of whcih is important to distinguish H3K9 from H3K27
and H4K20 (PubMed:18215768). {ECO:0000269|PubMed:11713521,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12679815,
ECO:0000269|PubMed:12887903, ECO:0000269|PubMed:18215768}.
-!- CATALYTIC ACTIVITY:
Reaction=L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) +
N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-
homocysteine; Xref=Rhea:RHEA:60276, Rhea:RHEA-COMP:15538, Rhea:RHEA-
COMP:15546, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.355;
Evidence={ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12679815,
ECO:0000269|PubMed:12887903};
-!- INTERACTION:
Q8X225; Q96UA9: 9G6.050; Xeno; NbExp=2; IntAct=EBI-1268994, EBI-15849296;
Q8X225; P07041: hh3; NbExp=2; IntAct=EBI-1268994, EBI-1270655;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
-!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that are
arranged in a triangular cluster; some of these Cys residues contribute
to the binding of two zinc ions within the cluster.
{ECO:0000269|PubMed:12372305}.
-!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
superfamily. Histone-lysine methyltransferase family. Suvar3-9
subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
-!- SEQUENCE CAUTION:
Sequence=AAL35215.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=CAF06044.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
---------------------------------------------------------------------------
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EMBL; AF419248; AAL35215.1; ALT_SEQ; Genomic_DNA.
EMBL; BX908809; CAF06044.1; ALT_SEQ; Genomic_DNA.
EMBL; CM002239; EAA28243.2; -; Genomic_DNA.
RefSeq; XP_957479.2; XM_952386.3.
PDB; 1ML9; X-ray; 1.98 A; A=30-331.
PDB; 1PEG; X-ray; 2.59 A; A/B=30-331.
PDBsum; 1ML9; -.
PDBsum; 1PEG; -.
SMR; Q8X225; -.
DIP; DIP-39600N; -.
IntAct; Q8X225; 2.
ChEMBL; CHEMBL3309062; -.
PRIDE; Q8X225; -.
EnsemblFungi; EAA28243; EAA28243; NCU04402.
GeneID; 3873656; -.
KEGG; ncr:NCU04402; -.
EuPathDB; FungiDB:NCU04402; -.
HOGENOM; CLU_020840_11_0_1; -.
InParanoid; Q8X225; -.
KO; K11419; -.
OMA; YAYHTHG; -.
EvolutionaryTrace; Q8X225; -.
Proteomes; UP000001805; Chromosome 4, Linkage Group IV.
Proteomes; UP000001805; Unassembled WGS sequence.
GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:InterPro.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR007728; Pre-SET_dom.
InterPro; IPR001214; SET_dom.
Pfam; PF05033; Pre-SET; 1.
Pfam; PF00856; SET; 1.
SMART; SM00468; PreSET; 1.
SMART; SM00317; SET; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS50867; PRE_SET; 1.
PROSITE; PS50280; SET; 1.
1: Evidence at protein level;
3D-structure; Chromosome; Metal-binding; Methyltransferase; Nucleus;
Reference proteome; S-adenosyl-L-methionine; Transferase; Zinc.
CHAIN 1..331
/note="Histone-lysine N-methyltransferase, H3 lysine-9
specific dim-5"
/id="PRO_0000186062"
DOMAIN 77..159
/note="Pre-SET"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
DOMAIN 162..297
/note="SET"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
DOMAIN 315..331
/note="Post-SET"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
REGION 172..174
/note="S-adenosyl-L-methionine binding"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
REGION 254..255
/note="S-adenosyl-L-methionine binding"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
METAL 79
/note="Zinc 1"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 79
/note="Zinc 2"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 81
/note="Zinc 1"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 87
/note="Zinc 1"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 87
/note="Zinc 3"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 92
/note="Zinc 1"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 94
/note="Zinc 2"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 141
/note="Zinc 2"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 141
/note="Zinc 3"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 145
/note="Zinc 2"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 147
/note="Zinc 3"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 151
/note="Zinc 3"
/evidence="ECO:0000244|PDB:1ML9, ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12372305, ECO:0000269|PubMed:12887903"
METAL 257
/note="Zinc 4"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
METAL 319
/note="Zinc 4"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
METAL 321
/note="Zinc 4"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
METAL 326
/note="Zinc 4"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
BINDING 215
/note="S-adenosyl-L-methionine"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
BINDING 217
/note="S-adenosyl-L-methionine"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
BINDING 251
/note="S-adenosyl-L-methionine"
/evidence="ECO:0000244|PDB:1PEG,
ECO:0000269|PubMed:12887903"
SITE 209
/note="Interacts with H3S10"
/evidence="ECO:0000269|PubMed:18215768"
SITE 227
/note="Interacts with H3R8"
/evidence="ECO:0000269|PubMed:18215768"
MUTAGEN 191
/note="Y->F: Reduces enzyme activity by 97%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 191
/note="Y->V: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 222
/note="D->E: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 222
/note="D->K: Reduces enzyme activity by 97%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 222
/note="D->Q: Reduces enzyme activity by 97%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 251
/note="R->H: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12372305"
MUTAGEN 254
/note="N->Q: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12372305"
MUTAGEN 255
/note="H->K: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12372305"
MUTAGEN 281
/note="F->Y: Converts the product-specificity of the HKMT
from H3K9me3 to H3K9me1/2."
/evidence="ECO:0000269|PubMed:15590646"
MUTAGEN 294
/note="F->W: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 294
/note="F->Y: Reduces enzyme activity by 20%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 296
/note="Y->F: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12372305"
MUTAGEN 330
/note="L->A: Reduces enzyme activity by over 99%."
/evidence="ECO:0000269|PubMed:12887903"
MUTAGEN 331
/note="W->A: Reduces enzyme activity by 97%."
/evidence="ECO:0000269|PubMed:12887903"
STRAND 41..44
/evidence="ECO:0000244|PDB:1ML9"
STRAND 46..49
/evidence="ECO:0000244|PDB:1ML9"
HELIX 73..75
/evidence="ECO:0000244|PDB:1ML9"
HELIX 86..88
/evidence="ECO:0000244|PDB:1ML9"
HELIX 93..95
/evidence="ECO:0000244|PDB:1ML9"
STRAND 96..98
/evidence="ECO:0000244|PDB:1PEG"
STRAND 115..118
/evidence="ECO:0000244|PDB:1ML9"
STRAND 119..121
/evidence="ECO:0000244|PDB:1PEG"
TURN 122..125
/evidence="ECO:0000244|PDB:1PEG"
HELIX 129..134
/evidence="ECO:0000244|PDB:1ML9"
HELIX 155..158
/evidence="ECO:0000244|PDB:1ML9"
STRAND 164..168
/evidence="ECO:0000244|PDB:1ML9"
STRAND 170..172
/evidence="ECO:0000244|PDB:1ML9"
STRAND 174..177
/evidence="ECO:0000244|PDB:1ML9"
STRAND 187..190
/evidence="ECO:0000244|PDB:1ML9"
STRAND 194..196
/evidence="ECO:0000244|PDB:1ML9"
HELIX 198..207
/evidence="ECO:0000244|PDB:1ML9"
HELIX 210..212
/evidence="ECO:0000244|PDB:1ML9"
HELIX 214..217
/evidence="ECO:0000244|PDB:1ML9"
STRAND 218..220
/evidence="ECO:0000244|PDB:1ML9"
STRAND 227..230
/evidence="ECO:0000244|PDB:1ML9"
HELIX 232..235
/evidence="ECO:0000244|PDB:1ML9"
STRAND 240..242
/evidence="ECO:0000244|PDB:1ML9"
STRAND 244..247
/evidence="ECO:0000244|PDB:1ML9"
HELIX 249..252
/evidence="ECO:0000244|PDB:1ML9"
STRAND 260..269
/evidence="ECO:0000244|PDB:1ML9"
HELIX 270..275
/evidence="ECO:0000244|PDB:1ML9"
STRAND 277..284
/evidence="ECO:0000244|PDB:1ML9"
STRAND 291..294
/evidence="ECO:0000244|PDB:1ML9"
SEQUENCE 331 AA; 37572 MW; 2C97AB4B5E582D88 CRC64;
MEKAFRPHFF NHGKPDANPK EKKNCHWCQI RSFATHAQLP ISIVNREDDA FLNPNFRFID
HSIIGKNVPV ADQSFRVGCS CASDEECMYS TCQCLDEMAP DSDEEADPYT RKKRFAYYSQ
GAKKGLLRDR VLQSQEPIYE CHQGCACSKD CPNRVVERGR TVPLQIFRTK DRGWGVKCPV
NIKRGQFVDR YLGEIITSEE ADRRRAESTI ARRKDVYLFA LDKFSDPDSL DPLLAGQPLE
VDGEYMSGPT RFINHSCDPN MAIFARVGDH ADKHIHDLAL FAIKDIPKGT ELTFDYVNGL
TGLESDAHDP SKISEMTKCL CGTAKCRGYL W


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CSB-EL016100MO Mouse Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific(NSD1) ELISA kit 96T
CSB-EL016100HU Human Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific(NSD1) ELISA kit 96T
EIAAB37976 H3-K4-HMTase SETD7,Histone H3-K4 methyltransferase SETD7,Histone-lysine N-methyltransferase SETD7,Kiaa1717,Mouse,Mus musculus,SET domain-containing protein 7,Set7,SET7_9,Set9,Setd7
EIAAB40613 H3-K9-HMTase 1,Histone H3-K9 methyltransferase 1,Histone-lysine N-methyltransferase SUV39H1,Mouse,Mus musculus,Position-effect variegation 3-9 homolog,Su(var)3-9 homolog 1,Suppressor of variegation 3-
EIAAB27930 Androgen receptor coactivator 267 kDa protein,Androgen receptor-associated protein of 267 kDa,ARA267,H3-K36-HMTase,H4-K20-HMTase,Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 speci
NSD1_MOUSE Mouse ELISA Kit FOR Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific 96T
EIAAB40617 H3-K9-HMTase 2,Histone H3-K9 methyltransferase 2,Histone-lysine N-methyltransferase SUV39H2,Mouse,Mus musculus,Su(var)3-9 homolog 2,Suppressor of variegation 3-9 homolog 2,Suv39h2
EIAAB37978 H4-K20-HMTase SETD8,Histone-lysine N-methyltransferase SETD8,Mouse,Mus musculus,N-lysine methyltransferase SETD8,PR_SET domain-containing protein 07,PR_SET07,PR-Set7,SET domain-containing protein 8,Se
EIAAB37979 Bos taurus,Bovine,H4-K20-HMTase SETD8,Histone-lysine N-methyltransferase SETD8,N-lysine methyltransferase SETD8,PR_SET domain-containing protein 07,PR_SET07,PR-Set7,SET domain-containing protein 8,SET