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Aliases & Descriptions for KDM4D
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
|
| Aliases |
|---|
| EC 1.14.11.- 3 | | FLJ10251 1, 2 | | JHDM3D 3 | | JMJD2D 2, 3 | | MGC141909 2 |
| | | Descriptions |
|---|
| JmjC domain-containing histone demethylation protein 3D 3 | | Jumonji domain-containing protein 2D 3 | | jumonji domain containing 2D 1, 2 | | lysine (K)-specific demethylase 4D 2 | | lysine-specific demethylase 4D 1 |
|
| | Search outside databases for aliases for KDM4D gene |
Summaries for KDM4D(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinateGene Wiki entry for KDM4D (JMJD2D) |
Genomic Location for KDM4D
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to
UCSC and
Ensembl,
Transcription factor binding sites according to
SABiosciences) About This Section
| Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 11q21 Ensembl cytogenetic band: 11q21 HGNC cytogenetic band: 11q21KDM4D Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different)
 GeneLoc gene densities for chromosome 11 GeneLoc Exon Structure GeneLoc location for GC11P094347:
(about GC identifiers)
Start:
|
94,346,493 bp from pter |
End:
|
94,372,326 bp from pter |
Size:
|
25,834 bases |
Orientation:
|
plus strand |
RefSeq DNA sequence:- NC_000011.8 NT_008984.17
| Proteins for KDM4D
(According to
1UniProtKB,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Enzo Life Sciences,
Abnova,
OriGene and/or,
Abcam,
Biochemical Assays by
Invitrogen,
Millipore,
R&D Systems,
Cell Signaling Technology, and/or
Enzo Life Sciences,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene,
Antibodies by Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Cell Signaling Technology,
Abcam,
Abnova, and/or
Novus Biologicals)
About This Section
| UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6 (See
protein sequence)Recommended Name: Lysine-specific demethylase 4D Size: 523 amino acids; 58603 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Nucleus (By similarity)
Caution: It is uncertain whether Met-1 or Met-4 is the initiator
Secondary accessions: B3KPC4 Q0VF39 Q9NT41 Q9NW76REFSEQ proteins: NP_060509.2
ENSEMBL proteins: ENSP00000334181
Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
1 Gene Ontology (GO) cellular component term (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- | About this table
Antibodies for KDM4D: Assays for KDM4D: | Protein
Domains/ Families for KDM4D(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry Q6B0I6
ProtoNet protein and cluster: Q6B0I6 1 Blocks protein family: IPB003347 Transcription factor jumonji
UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6Similarity: Belongs to the JHDM3 histone demethylase familySimilarity: Contains 1 JmjC domainSimilarity: Contains 1 JmjN domain | Gene Function for KDM4D
(According to MGI Jun 06 2009, UniProtKB,
IUBMB,and/or Genatlas,
shRNA from
OriGene,
Sigma-Aldrich, RNAi from
Sigma-Aldrich,
RNAi Products,
Clones, and
Q-PCR Products
from Invitrogen,
Millipore,
OriGene, and/or
Abnova,
siRNAs from
Applied Biosystems,
SYBR primers from OriGene,
Cell-based Assays from Millipore,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_018039
Applied Biosystems Silencer® siRNAs for KDM4D
Sigma-Aldrich siRNA for KDM4D  Sigma-Aldrich shRNA for KDM4D  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_018039                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_018039                                  untagged cDNA clones in CMV expression vector (see all 2): AK056162 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_018039
UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinateEnzyme Number (IUBMB): EC 1.14.11.- 1 MGI phenotypic allele for Kdm4d (no phenotypes)
5 Gene Ontology (GO) molecular function terms (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005506 | iron ion binding |
IEA | -- | | GO:0008270 | zinc ion binding |
IEA | -- | | GO:0016491 | oxidoreductase activity |
IEA | -- | | GO:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
IEA | -- | | GO:0046872 | metal ion binding |
IEA | -- | About this table | Pathways & Interactions for KDM4D
(Pathways according to Invitrogen
(maps by GeneGo),
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Proteins Network according to
SABiosciences,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|
Gene Network CentralTM Interacting Genes and Proteins Network for KDM4D 
1 Interacting protein for KDM4D (ENSP000003341813) via UniProtKB, MINT, and/or STRINGAbout this table
4 Gene Ontology (GO) biological process terms (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006350 | transcription |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
IEA | -- | | GO:0016568 | chromatin modification |
IEA | -- | | GO:0055114 | oxidation reduction |
IEA | -- | About this table
|
Drugs & Compounds for KDM4D(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
Browse Tocris compounds for KDM4D
|
Transcripts for KDM4D(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank, RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from Invitrogen,
Millipore, and/or
Abnova,
siRNAs from Applied Biosystems,
Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
Tagged/untagged cDNA clones from
OriGene, Expression Assays from Applied Biosystems) About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_018039
Sigma-Aldrich siRNA for KDM4D  Sigma-Aldrich shRNA for KDM4D  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_018039 REFSEQ mRNAs for KDM4D gene: NM_018039.2
Applied Biosystems TaqMan ® Gene Expression Assays: NM_018039               OriGene GFP tagged cDNA clone in CMV expression vector: NM_018039                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_018039                                  untagged cDNA clones in CMV expression vector (see all 2): AK056162  Additional cDNA sequence: AK001113.1 AK056162.1 AL137545.1 BC031862.1 BC074739.2 BC119010.1 BC122858.1 1 DOTS entry: DT.106378 24/26 AceView cDNA sequences (see all 26
):AW593120 AU120493 AW339850 BC074739 NM_018039 AA732856 AK056162 AU149055 CA311555 BQ006169 BC031862 AA435771 AI467798 AA236569 AL137545 AK001113 AA234602 AA758505 BG719158 BE719807 BE719813 AU153509 BX283998 BE719808 Unigene Cluster for KDM4D: Lysine (K)-specific demethylase 4D Hs.503598 [show with all ESTs]Unigene Representative Sequence: NM_018039
GeneLoc Exon Structure
1 Ensembl transcript including schematic representation: ENST00000335080
|
Expression for KDM4D
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Expression Assays from
Applied Biosystems
)
About This Section
| KDM4D expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for KDM4D
1 / 2 6 probe-sets matching KDM4D gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: GTAGTTTTCA
SOURCE GeneReport for Unigene cluster: Hs.503598
|
Orthologs for KDM4D
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for KDM4D gene from 4 species
About this table Species with no ortholog for KDM4D
ENSEMBL Gene Tree for KDM4D | Paralogs for KDM4D(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| Paralogs for KDM4D gene
- KDM4A2 JARID22 KDM4C2 KDM4B2
|
SNPs/Variants for KDM4D(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
|
HapMap Linkage Disequilibrium images for KDM4D (up to first 250kb)
|
Disorders & Mutations for KDM4D
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
HGMD, GAD,
HuGE Navigator,
BCGD,
and/or TGDB.)
About This Section
|
OMIM: 609766
|
Medical News for KDM4D(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for KDM4D (in
PubMed.
Associations of this gene to articles via
1Novoseek,
2HGNC,
3Entrez Gene,
4UniProtKB/Swiss-Prot,
5UniProtKB/TrEMBL,
6GAD, and/or
7PharmGKB)
About This Section
| 10 PubMed articles for KDM4D gene:- Identification and characterization of JMJD2 family genes in silico. (PubMed id 15138608)1, 2, 3, 4 Katoh M. and Katoh M. (2004)
- Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PubMed id 16603238)3, 4 Whetstine J.R.... Shi Y. (2006)
- Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)3, 4 Taylor T.D....Sakaki Y. (2006)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)3, 4 Gerhard D.S....Malek J. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)3, 4 Ota T....Sugano S. (2004)
- Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (PubMed id 18951430)3 Anney R.J....Gill M. (2008)
- Activation of androgen receptor by histone demethylases JMJD2A and JMJD2D. (PubMed id 17555712)3 Shin S. and Janknecht R. (2007)
- The full-ORF clone resource of the German cDNA Consortium. (PubMed id 17974005)4 Bechtel S....Schupp I. (2007)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)3 Strausberg R.L....Marra M.A. (2002)
- Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)3 Bonaldo M.F....Soares M.B. (1996)
|
Search for KDM4D
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing KDM4D
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing KDM4D
(According to HUGE)
About This Section
| -- |
Specialized Databases showing KDM4D(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL, Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot) About This Section
|
| About This Section
| --
| Services for KDM4D(Reagents available from Applied Biosystems, Antibodies and assays by Cell
Signaling Technology, Abcam, Novus Biologicals, Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich, Enzo Life Sciences, and/or Tocris Bioscience) About This Section
| 
 Products for KDM4D:

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GeneCards Homepage - Last full update: 2 Jul 2009
Incremental update: 13 Oct 2009
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