BRENDA - Enzyme Database show
show all sequences of 1.14.11.27

Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family

Hillringhaus, L.; Yue, W.W.; Rose, N.R.; Ng, S.S.; Gileadi, C.; Loenarz, C.; Bello, S.H.; Bray, J.E.; Schofield, C.J.; Oppermann, U.; J. Biol. Chem. 286, 41616-41625 (2011)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of N-terminally His-tagged KDM4A in Escherichia coli; expression of N-terminally His-tagged KDM4B in Escherichia coli; expression of N-terminally His-tagged KDM4C in Escherichia coli
Homo sapiens
Crystallization (Commentary)
Crystallization
Organism
purified recombinant KDM4C, sitting drop vapor diffusion method, mixing of 7 mg/ml protein with 2 mM N-oxalylglycine with well solution, containing 25% v/v PEG 3350, 0.2 M sodium nitrate, 0.1 M Bis tris propane, pH 6.5, 5% v/v ethylene glycol, 0.01 M NiCl2, in a 2:1 ratio, 4C, X-ray diffraction structure determination and analysis at 2.55 A resolution
Homo sapiens
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
nucleus
-
Homo sapiens
5634
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Zn2+
structure of Zn2+ binding sites of the isozymes, overview; structure of Zn2+ binding sites of the isozymes, overview; structure of Zn2+ binding sites of the isozymes, overview
Homo sapiens
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Homo sapiens
-
KDM4B
-
Homo sapiens
O75164
KDM4A; KDM4A
-
Homo sapiens
Q9H3R0
KDM4C; KDM4C
-
Purification (Commentary)
Commentary
Organism
recombinant N-terminally His-tagged KDM4A from Escherichia coli by nickel affinity chromatography; recombinant N-terminally His-tagged KDM4B from Escherichia coli by nickel affinity chromatography; recombinant N-terminally His-tagged KDM4C from Escherichia coli by nickel affinity chromatography
Homo sapiens
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
-
725450
Homo sapiens
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
substrate is preferred compared to histone H3-N6,N6-dimethyl-L-lysine36
725450
Homo sapiens
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
-
725450
Homo sapiens
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
low activity
725450
Homo sapiens
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
additional information
KDM4D and -E only act on H3K9, with no evidence for demethylation of H3K36, while KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates. No activity by all isozymes with H3K4me3, H3K9me1, and H3K27me3
725450
Homo sapiens
?
-
-
-
-
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of N-terminally His-tagged KDM4B in Escherichia coli
Homo sapiens
expression of N-terminally His-tagged KDM4A in Escherichia coli
Homo sapiens
expression of N-terminally His-tagged KDM4C in Escherichia coli
Homo sapiens
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant KDM4C, sitting drop vapor diffusion method, mixing of 7 mg/ml protein with 2 mM N-oxalylglycine with well solution, containing 25% v/v PEG 3350, 0.2 M sodium nitrate, 0.1 M Bis tris propane, pH 6.5, 5% v/v ethylene glycol, 0.01 M NiCl2, in a 2:1 ratio, 4C, X-ray diffraction structure determination and analysis at 2.55 A resolution
Homo sapiens
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
nucleus
-
Homo sapiens
5634
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Zn2+
structure of Zn2+ binding sites of the isozymes, overview
Homo sapiens
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminally His-tagged KDM4A from Escherichia coli by nickel affinity chromatography
Homo sapiens
recombinant N-terminally His-tagged KDM4B from Escherichia coli by nickel affinity chromatography
Homo sapiens
recombinant N-terminally His-tagged KDM4C from Escherichia coli by nickel affinity chromatography
Homo sapiens
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
-
725450
Homo sapiens
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
substrate is preferred compared to histone H3-N6,N6-dimethyl-L-lysine36
725450
Homo sapiens
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
-
725450
Homo sapiens
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
low activity
725450
Homo sapiens
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
?
additional information
KDM4D and -E only act on H3K9, with no evidence for demethylation of H3K36, while KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates. No activity by all isozymes with H3K4me3, H3K9me1, and H3K27me3
725450
Homo sapiens
?
-
-
-
-
General Information
General Information
Commentary
Organism
evolution
human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone, structural and phylogenetic analysis, overview. KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates, substrate selectivity of the human KDM4 histone demethylase subfamily, overview; human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone, structural and phylogenetic analysis, overview. KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates, substrate selectivity of the human KDM4 histone demethylase subfamily, overview; human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone, structural and phylogenetic analysis, overview. KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates, substrate selectivity of the human KDM4 histone demethylase subfamily, overview
Homo sapiens
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview; substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview; substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview
Homo sapiens
General Information (protein specific)
General Information
Commentary
Organism
evolution
human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone, structural and phylogenetic analysis, overview. KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates, substrate selectivity of the human KDM4 histone demethylase subfamily, overview
Homo sapiens
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview
Homo sapiens
Other publictions for EC 1.14.11.27
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
743916
Hancock
The activity of JmjC histone ...
Homo sapiens
ACS Chem. Biol.
12
1011-1019
2017
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1
1
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1
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1
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1
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1
1
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1
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1
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-
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-
-
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2
2
-
-
-
745949
An
HistoneH3 demethylase JMJD2A ...
Homo sapiens
Oncotarget
8
49093-49109
2017
-
-
1
-
1
-
-
-
-
-
-
1
-
1
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4
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1
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4
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1
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2
2
-
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-
744722
Morera
4-biphenylalanine- and 3-phen ...
Homo sapiens
ChemMedChem
11
2063-2083
2016
1
-
1
-
-
-
33
1
-
1
-
2
-
2
-
-
1
1
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2
-
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4
-
1
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1
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30
1
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1
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30
33
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1
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1
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2
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1
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2
-
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4
-
1
-
-
-
1
-
-
-
-
2
2
-
-
-
744785
Pedersen
Continual removal of H3K9 pro ...
Mus musculus, Mus musculus C57BL/6
EMBO J.
35
1550-1564
2016
-
-
1
-
-
-
-
-
2
1
-
8
-
5
-
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1
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8
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2
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4
2
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8
-
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-
-
2
-
-
8
-
-
-
-
-
-
-
-
-
-
3
6
-
-
-
745803
Gacek-Matthews
KdmA, a histone H3 demethylas ...
Aspergillus nidulans, Aspergillus nidulans WIM126
Mol. Microbiol.
96
839-860
2015
-
-
1
-
1
-
-
-
1
1
-
4
-
3
-
-
-
-
-
-
-
-
6
-
1
-
-
-
-
-
-
-
-
-
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-
1
-
-
1
-
-
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1
1
-
4
-
-
-
-
-
-
-
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6
-
1
-
-
-
-
-
-
-
-
3
3
-
-
-
744589
Ryu
Yeast histone H3 lysine 4 dem ...
Saccharomyces cerevisiae
BMC Biol.
12
75
2014
-
-
1
-
1
-
-
-
-
1
-
7
-
3
-
-
-
-
-
-
-
-
7
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
3
-
-
-
-
-
-
3
-
7
-
-
-
-
-
-
-
-
7
-
-
-
-
-
-
-
-
-
-
3
9
-
-
-
745919
Kupershmit
KDM4C (GASC1) lysine demethyl ...
Homo sapiens
Nucleic Acids Res.
42
6168-6182
2014
-
-
1
-
3
-
-
-
2
-
-
4
-
5
-
-
-
-
-
4
-
-
5
1
-
-
-
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4
-
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4
-
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4
-
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4
-
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-
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16
-
-
5
4
-
-
-
-
-
-
-
-
-
3
12
-
-
-
724709
Black
KDM4A lysine demethylase induc ...
Homo sapiens
Cell
154
541-555
2013
-
-
1
-
2
-
-
-
1
-
-
1
-
1
-
-
-
-
-
3
-
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1
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1
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2
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1
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1
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-
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3
-
-
1
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
724813
Crona
Gene regulation by the lysine ...
Drosophila melanogaster
Dev. Biol.
373
453-463
2013
-
-
1
-
2
-
-
-
1
-
-
1
-
3
-
-
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1
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1
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2
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-
-
-
-
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3
3
-
-
-
724815
Ishimura
Jmjd5, an H3K36me2 histone dem ...
Mus musculus
Development
139
749-759
2012
-
-
1
-
2
-
-
-
1
-
-
1
-
3
-
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2
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1
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1
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2
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1
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1
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2
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1
-
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-
-
-
-
-
-
-
4
4
-
-
-
725960
Del Rizzo
Crystal structure and function ...
Homo sapiens
Mol. Cell. Biol.
32
4044-4052
2012
-
-
1
1
-
-
-
-
-
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1
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2
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1
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1
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1
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1
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1
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1
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1
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1
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1
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3
3
-
-
-
726260
Pan
The histone demethylase Jhdm1a ...
Homo sapiens, Mus musculus, Mus musculus C57/BL6J
PLoS Genet.
8
e1002761
2012
-
-
2
-
3
-
-
-
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6
-
62
-
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3
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10
-
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2
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6
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3
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10
-
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-
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-
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5
5
-
-
-
726301
Lin
HP1a targets the Drosophila KD ...
Drosophila melanogaster
PLoS ONE
7
e39758
2012
1
-
1
-
2
-
-
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1
-
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1
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4
-
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1
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1
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1
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2
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1
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1
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1
1
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-
712996
Peng
Molecular characterization of ...
Sus scrofa
Mol. Biol. Rep.
38
4697-4704
2011
-
-
1
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4
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6
-
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1
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6
-
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-
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-
-
-
-
-
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-
-
1
1
-
-
-
724651
He
KDM2b/JHDM1b, an H3K36me2-spec ...
Homo sapiens
Blood
117
3869-3880
2011
-
-
-
-
1
-
-
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1
-
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1
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2
-
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1
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2
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1
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1
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1
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1
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2
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3
3
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725450
Hillringhaus
Structural and evolutionary ba ...
Homo sapiens
J. Biol. Chem.
286
41616-41625
2011
-
-
1
1
-
-
-
-
1
1
-
5
-
6
-
-
1
-
-
-
-
-
12
-
-
-
-
-
-
-
-
-
-
-
-
-
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3
-
1
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