KDM4D Gene
protein-coding GIFtS: 51
GCID: GC11P094706
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|
lysine (K)-specific demethylase 4D(Previous name: jumonji domain containing 2D )
(Previous symbol: JMJD2D)
| |
Aliases
for KDM4D gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Lysine (K)-Specific Demethylase 4D1 2 | | FLJ102511 | | JMJD2D1 2 3 5 | | Lysine-Specific Demethylase 4D2 | | Jumonji Domain Containing 2D1 2 | | EC 1.14.11.-3 | | JmjC Domain-Containing Histone Demethylation Protein 3D2 3 | | JHDM3D3 | | Jumonji Domain-Containing Protein 2D2 3 | | EC 1.14.118 |
Export aliases for KDM4D gene to outside databasesPrevious GC identifers: GC11P094347 GC11P090771 |
Summaries
for KDM4D gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
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 inhistone 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 Lysresidue generates formaldehyde and succinate
Gene Wiki entry for KDM4D (JMJD2D)
|
Genomic Views
for KDM4D gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000011.9 NC_018922.1 NT_167190.1
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the KDM4D gene promoter:
Sp1 AP-1 RREB-1 Nkx2-2 ATF-2 Nkx2-5 POU6F1 (c2) S8 c-Jun En-1
Other transcription factors
Search SABiosciences Chromatin IP Primers for KDM4D
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat KDM4D |
Genomic Location:
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 information about chromosome 11 GeneLoc Exon Structure GeneLoc location for GC11P094706: view genomic region
(about GC identifiers)
Start:
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94,706,845 bp from pter |
End:
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94,732,682 bp from pter |
Size:
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25,838 bases |
Orientation:
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plus strand |
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Proteins
for KDM4D gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
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
Sequence caution: Sequence=BAA91508.1; Type=Erroneous initiation;
4 PDB 3D structures from  and Proteopedia  for KDM4D:3DXT (3D)
3DXU (3D)
4HON (3D)
4HOO (3D)
Secondary accessions: B3KPC4 Q0VF39 Q9NT41 Q9NW76Explore the universe of human proteins at neXtProt for KDM4D: NX_Q6B0I6
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q6B0I6
4/5 DME Specific Peptides for KDM4D (Q6B0I6) (see all 5)
KDM4D Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_060509.2
ENSEMBL proteins: ENSP00000334181 ENSP00000460897
Human Recombinant Protein Products for KDM4D:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- |
KDM4D for ontologies About GeneDecksing
KDM4D Antibody Products:
Assay Products for KDM4D: |
Protein
Domains /
Families
for KDM4D gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
KDM4D for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q6B0I6ProtoNet 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 |
Function
for KDM4D gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: KDM4D_HUMAN, Q6B0I6Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role inhistone 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 Lysresidue generates formaldehyde and succinate Enzyme Numbers (IUBMB): EC 1.14.11.-1 EC 1.14.112
Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| 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 | -- |
KDM4D for ontologies About GeneDecksing
Phenotypes:
1 GenomeRNAi human phenotype for KDM4D:
6 MGI mutant phenotypes (inferred from 2 alleles ) (MGI details for Kdm4d):
KDM4D for phenotypes About GeneDecksing
Animal Models:
Mouse knock-out Kdm4dtm1Zuk for KDM4D
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for KDM4D (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for KDM4D
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: KDM4D (NM_018039) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for KDM4D | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM4D |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM4D |
|
Pathways & Interactions
for KDM4D gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for KDM4D
STRING Interaction
Network Preview (showing 3 interactants - click image to see more details)
3 Interacting proteins for KDM4D (Q6B0I63 ENSP000003341814) via UniProtKB, MINT, STRING, and/or I2DAbout this table
Gene Ontology (GO): 3 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006351 | transcription, DNA-dependent |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
IEA | -- | | GO:0016568 | chromatin modification |
IEA | -- |
KDM4D for ontologies About GeneDecksing
|
Drugs & Compounds
for KDM4D gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for KDM4D
Search CenterWatch for drugs/clinical trials and news about KDM4D
|
Transcripts
for KDM4D gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for KDM4D gene: NM_018039.2 Unigene Cluster for KDM4D: Lysine (K)-specific demethylase 4D Hs.503598 [show with all ESTs]Unigene Representative Sequence: NM_0180392 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000335080(uc001pfe.3) ENST00000536741
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for KDM4D (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for KDM4D
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: KDM4D (NM_018039) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for KDM4D | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM4D |
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): AU149055 AA732856 AW593120 NM_018039 AU120493 BC074739 AW339850 AK056162 CA311555 AK001113 BC031862 AA758505 AI467798 BQ006169 AA435771 AA234602 AL137545 AA236569 AU153509 BE719813 BE719807 BG719158 AU146540 BE719808
GeneLoc Exon Structure
|
Expression
for KDM4D gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| KDM4D expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GTAGTTTTCA
About this image
See KDM4D Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for KDM4D
SOURCE GeneReport for Unigene cluster: Hs.503598
SABiosciences Custom PCR Arrays for KDM4D
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for KDM4D
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat KDM4D | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat KDM4D | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat KDM4D | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM4D |
Orthologs
for KDM4D gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for KDM4D gene from 6/22 species (see all 22) About this table
ENSEMBL Gene Tree for KDM4D (if available)
TreeFam Gene Tree for KDM4D (if available) |
Paralogs
for KDM4D gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for KDM4D gene
- KDM4A2 KDM4C2 KDM4E2 KDM4B2
5 SIMAP similar genes for KDM4D using alignment to 1 protein entry: KDM4D_HUMAN:KDM4A KDM4E KDM4C KDM4B JMJD2B
KDM4D for paralogs About GeneDecksing
3 Pseudogenes.org Pseudogenes for KDM4D
PGOHUM00000242864 PGOHUM00000242865 PGOHUM00000242869
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Genomic Variants
for KDM4D gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 11 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for KDM4D (94706845 - 94732682 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for KDM4D: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing KDM4D |
|
Disorders
/ Diseases
for KDM4D gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
KDM4D for disorders About GeneDecksing
OMIM gene information: 609766
OMIM disorders: --
4  diseases for KDM4D: About MalaCardsconduct disorder adhd retinoblastoma malaria
Human Genome Epidemiology (HuGE) Navigator: KDM4D (1 document)
Export disorders for KDM4D gene to outside databases
|
Publications
for KDM4D gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for KDM4D gene, integrated from 9 sources (see all 14):
(articles sorted by number of sources associating them with KDM4D) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Identification and characterization of JMJD2 family genes in silico. (PubMed id 15138608)1, 2, 3, 9 Katoh M. and Katoh M. (2004)
- Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PubMed id 16603238)1, 2 Whetstine J.R.... Shi Y. (2006)
- Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)1, 2 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)1, 2 Gerhard D.S....Malek J. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Poly (ADP-ribose) glycohydrolase regulates retinoic acid receptor- mediated gene expression. (PubMed id 23102699)2 Le May N.... Coin F. (2012)
- Regulation of tumor suppressor p53 and HCT116 cell phy siology by histone demethylase JMJD2D/KDM4D. (PubMed id 22514644)1 Kim T.D....Janknecht R. (2012)
- Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
- Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (PubMed id 18951430)1 Anney R.J....Gill M. (2008)
- Activation of androgen receptor by histone demethylases JMJD2A and JMJD2D. (PubMed id 17555712)1 Shin S. and Janknecht R. (2007)
|
External Searches for KDM4D gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing KDM4D gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing KDM4D gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing KDM4D gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for KDM4D | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for KDM4D gene:
Search GeneIP for patents involving KDM4D
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for KDM4D gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
| | |  | OriGene Antibodies for KDM4D | | Browse OriGene shRNA RFPs | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for KDM4D | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for KDM4D | | | OriGene Protein Over-expression Lysate for KDM4D | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for KDM4D | | OriGene 3'-UTR Clone for KDM4D | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for KDM4D | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for KDM4D | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | Browse OriGene full length recombinant human proteins expressed in human HEK293 cells | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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 | | | KDM4D Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM4D |
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