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KDM4D Gene

protein-coding   GIFtS: 47

GC11P094347
lysine (K)-specific demethylase 4D
(Previous name: jumonji domain containing 2D )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: JMJD2D)
Services    
(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
External Ids
HGNC: 254981
Entrez Gene: 556932
UniProtKB: Q6B0I63
Ensembl: ENSG000001862807
Search outside databases for aliases for KDM4D gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6
Function: 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
succinate

Gene Wiki entry for KDM4D (JMJD2D)

(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: 11q21

KDM4D 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  
(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 Q9NW76

REFSEQ proteins: NP_060509.2  

ENSEMBL proteins: 
ENSP00000334181 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (KDM4D / JMJD2D)
Human Recombinant Proteins from Abnova (JMJD2D)
                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 IDQualified GO termEvidencePubMed IDs
GO:0005634 nucleus IEA--
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Antibodies for KDM4D: 
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Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for KDM4D
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Antibodies from Abcam (KDM4D / JMJD2D), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (JMJD2D)
Search Novus for antibodies for KDM4D

Assays for KDM4D: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

3 InterPro domains/families:
 IPR013129 TF_JmjC
 IPR003347 TF_JmjC_AAH
 IPR003349 TF_JmjN


   GeneDecks  KDM4D for the domains selected above  
About GeneDecksing

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, Q6B0I6
Similarity: Belongs to the JHDM3 histone demethylase family
Similarity: Contains 1 JmjC domain
Similarity: Contains 1 JmjN domain

(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

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (KDM4D)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              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  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              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, Q6B0I6
Function: 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
succinate
Enzyme 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 IDQualified GO termEvidencePubMed 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 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 STRING
InteractantInteraction Details
GeneCardExternal ID(s)
JMJD1CENSP000003359293STRING (score=.885)
About this table

4 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed 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
(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 drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds 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

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (KDM4D)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              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  
(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


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

83033_at2 U95-D 2 1.00 0.97 0.59 0.91 -- -- -- -- --

76276_at2 U95-D 1 0.94 1.00 0.85 1.10 -- -- -- -- --

220278_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

242788_at2 U133-B 1 0.91 1.00 -- -- -- -- -- -- --

220278_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

242788_at2 U133Plus2 1 0.91 1.00 -- -- -- -- -- -- --
About this table
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: GTAGTTTTCA

SOURCE GeneReport for Unigene cluster: Hs.503598
(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
Organism Gene Locus Description Human
Similarity
NCBI accessions
chimpanzee
(Pan troglodytes)
JMJD2D1   -- jumonji domain containing 2D 99.49(n)
99.43(a)
466754  XM_522154.2  XP_522154.1 
cow
(Bos taurus)
JMJD2D1   -- jumonji domain containing 2D 77.72(n)
78.28(a)
524768  XM_603100.2  XP_603100.2 
rat
(Rattus norvegicus)
LOC6895821   -- similar to jumonji domain containing 2D 74.24(n)
71.51(a)
689582  XM_001072078.1  XP_001072078.1 
mouse
(Mus musculus)
Kdm4d5
Jmjd2d1
95
lysine (K)-specific demethylase 4D5
jumonji domain containing 2D1
75.23(n)1
72.71(a)1
2446941  NM_173433.21  NP_775609.21 
 AK0300205  AK1552275  (see all 8)
About this table        Species with no ortholog for KDM4D

ENSEMBL Gene Tree for KDM4D
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for KDM4D gene
KDM4A2  JARID22  KDM4C2  KDM4B2  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/100 NCBI SNPs in KDM4D are shown (see all 100 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 71)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 11 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs10545321,2
A,C,F,H,O94372055(+) TTAGCG/ATAACC 1 -- ut31 ese35Minor allele frequency- A:0.07MN EU EA WA 602
rs37408531,2
C,F,H94371407(+) ACGCCA/GATCTG 1 R/Q mis1 ese318Minor allele frequency- N:0.00EA NA EU WA 3026
rs343660361,2
C,F94371595(+) CTCCAG/TCCAAG 1 A/S mis11Minor allele frequency- T:0.03NA 58
rs356315121,2
C,F94371249(+) GCCAGC/GCAAGA 1 S/R mis15Minor allele frequency- G:0.01NA EU EA WA 494
--
rs176800611,2
F,H94370760(+) TGGCAT/CACAGA 1 H/H syn1 ese37Minor allele frequency- C:0.01NA EU EA WA 554
rs9065301,2
A,C,F,O94351386(-) CCCAGC/TCTGGA 1 -- int13Minor allele frequency- T:0.45NA 136
rs123638721,2
A,C,F,H94368547(+) TTGACT/CAAATA 1 -- int14Minor allele frequency- C:0.47EU EA WA 410
rs110209921,2
A,C,F,H94349007(+) ttaccA/Ccaaaa 1 -- int14Minor allele frequency- C:0.47EU EA WA 416
rs47531581,2
A,C,F,H94366914(+) AGAGAG/ACACAC 1 -- int1 tfbs37Minor allele frequency- A:0.08NA EU EA WA 556
rs13859671,2
A,C,F,H94364648(+) ACTTCA/GTTTTT 1 -- int112Minor allele frequency- G:0.36NS EU EA WA NA 630
About this table

HapMap Linkage Disequilibrium images for KDM4D (up to first 250kb)

(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

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(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:
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 55693 HGNC: 25498 AceView: JMJD2D Ensembl:ENSG00000186280 euGenes: HUgn55693
ECgene: KDM4D H-InvDB: KDM4D
(According to HUGE)
About This Section

  --
(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

  --
(Available from WIS Yeda, Salk, Tufts)
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  --
(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:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
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 Predesigned and custom siRNAs for KDM4D Antibodies for KDM4D
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
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 Recombinant Proteins
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 Antibodies (KDM4D / JMJD2D)
 Search OriGene for KDM4D
 Search Tocris compounds for KDM4D




 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Search Novus for antibodies for KDM4D

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