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KDM4C Gene

protein-coding   GIFtS: 50

GC09P006747
lysine (K)-specific demethylase 4C
(Previous name: jumonji domain containing 2C )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: JMJD2C)
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
FLJ25949 2
GASC1 1, 2, 3
JHDM3C 2, 3
JMJD2C 2, 3
KIAA0780 1, 2, 3
OTTHUMP00000021052 2
OTTHUMP00000044461 2
bA146B14.1 2
Descriptions
GASC-1 protein 3
Gene amplified in squamous cell carcinoma 1 protein 3
JmjC domain-containing histone demethylation protein 3C 2, 3
Jumonji domain-containing protein 2C 3
gene amplified in squamous cell carcinoma 1 2
jumonji domain containing 2C 1, 2
lysine (K)-specific demethylase 4C 2
lysine-specific demethylase 4C 1
External Ids
HGNC: 170711
Entrez Gene: 230812
UniProtKB: Q9H3R03
Ensembl: ENSG000001070777
Search outside databases for aliases for KDM4C gene

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

EntrezGene summary for KDM4C:
This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein with one JmjC
domain, one JmjN domain, two PHD-type zinc fingers, and two Tudor domains. This nuclear protein
functions as a trimethylation-specific demethylase, converting specific trimethylated histone
residues to the dimethylated form. Chromosomal aberrations and increased transcriptional
expression of this gene are associated with esophageal squamous cell carcinoma. Alternative
splicing results in multiple transcript variants. [provided by RefSeq]

UniProtKB/Swiss-Prot: KDM4C_HUMAN, Q9H3R0
Function: Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of
histone H3, thereby playing a central role in histone code. Does not demethylate histone H3
'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36'
residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue
generates formaldehyde and succinate

Gene Wiki entry for KDM4C (JMJD2C)

(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: 9p24.1   Ensembl cytogenetic band:  9p24.1   HGNC cytogenetic band: 9p24-p23

KDM4C 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 9         GeneLoc Exon Structure

GeneLoc location for GC09P006747:     (about GC identifiers)

Start:
6,747,654 bp from pter
End:
7,165,648 bp from pter
Size:
417,995 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000009.10  NT_008413.17  
(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: KDM4C_HUMAN, Q9H3R0 (See protein sequence)
Recommended Name: Lysine-specific demethylase 4C  
Size: 1056 amino acids; 119982 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=CAI39533.1; Type=Erroneous gene model prediction; Sequence=CAI39608.1;
Type=Erroneous gene model prediction;
Secondary accessions: O94877 Q2M3M0 Q5JUC9 Q5VYJ2 Q5VYJ3
Alternative splicing: 2 isoforms:  Q9H3R0-1   Q9H3R0-2   

REFSEQ proteins (4 alternative transcripts): 
NP_001140166.1  NP_001140167.1  NP_001140168.1  NP_055876.2  


ENSEMBL proteins: 
ENSP00000370707 ENSP00000383990 ENSP00000370710 


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 (KDM4C / GASC1 / JMJD2C)
Browse Abnova for Human Recombinant Proteins
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005575 cellular_component ND--
GO:0005634 nucleus IEA--
About this table

Antibodies for KDM4C: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Browse Antibodies at Sigma-Aldrich
Browse R&D Systems for Antibodies
Antibodies from Abcam (KDM4C / GASC1 / JMJD2C), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (JMJD2C)
Novus Biologicals Antibody for JMJD2C

Assays for KDM4C: 
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

5/6 InterPro domains/families (see all 6 ):
 IPR001965 Znf_PHD
 IPR013129 TF_JmjC
 IPR003347 TF_JmjC_AAH
 IPR019786 Zinc_finger_PHD-type_CS
 IPR003349 TF_JmjN


   GeneDecks  KDM4C for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q9H3R0

ProtoNet protein and cluster: Q9H3R0

3 Blocks protein families:
IPB002999 Tudor domain
IPB003347 Transcription factor jumonji
IPB003349 Transcription factor jumonji


UniProtKB/Swiss-Prot: KDM4C_HUMAN, Q9H3R0
Domain: The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an
interdigitated structure and the unusual fold is required for its ability to bind methylated
histone tails (By similarity)
Similarity: Belongs to the JHDM3 histone demethylase family
Similarity: Contains 1 JmjC domain
Similarity: Contains 1 JmjN domain
Similarity: Contains 2 PHD-type zinc fingers
Similarity: Contains 2 Tudor domains

(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 (KDM4C)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (JMJD2C)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015061

              Applied Biosystems Silencer® siRNAs for KDM4C

              Sigma-Aldrich siRNA and siRNA Panels for KDM4C  
                     Sigma-Aldrich shRNA for KDM4C  
                     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_015061
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_015061
                                 untagged cDNA clone in CMV expression vector: NM_015061 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_015061

UniProtKB/Swiss-Prot: KDM4C_HUMAN, Q9H3R0
Function: Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of
histone H3, thereby playing a central role in histone code. Does not demethylate histone H3
'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36'
residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue
generates formaldehyde and succinate
Enzyme Number (IUBMB): EC 1.14.11.- 

5/8 Gene Ontology (GO) molecular function terms (links to tree view) (see all 8 ):

GO IDQualified GO termEvidencePubMed IDs
GO:0003674 molecular_function ND--
GO:0003676 nucleic acid binding IEA--
GO:0005506 iron ion binding IEA--
GO:0005515 protein binding IEA--
GO:0008270 zinc 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  KDM4C 

  --

5 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:0008150 biological_process ND--
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 KDM4C

(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 (KDM4C)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (JMJD2C)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015061

              Sigma-Aldrich siRNA and siRNA Panels for KDM4C  
                     Sigma-Aldrich shRNA for KDM4C  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_015061  

REFSEQ mRNAs for KDM4C gene (4 alternative transcripts): 

NM_001146694.1   NM_001146695.1   NM_001146696.1   NM_015061.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_015061  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_015061
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_015061
                                 untagged cDNA clone in CMV expression vector: NM_015061 

Additional cDNA sequence: 

AB018323.1 AB037901.1 AK098534.1 AK296401.1 AK303651.1 AK304032.1 AK304095.1 AK310439.1 
AK314355.1 BC008296.1 BC036628.2 BC042976.2 BC053678.1 BC060771.1 BC104859.1 BC104861.1 
BC143571.1 CR600819.1 

24/29 DOTS entries (see all 29 ):

DT.99981759  DT.100823066  DT.100823065  DT.91768275  DT.75169436  DT.91768266  DT.107530  DT.306886 
DT.100823069  DT.100823071  DT.40126457  DT.100024027  DT.101958301  DT.75135105  DT.99930232  DT.121146794 
DT.86846917  DT.91768262  DT.305092  DT.75105207  DT.75141359  DT.75181324  DT.100024026  DT.433347 

24/247 AceView cDNA sequences (see all 247 ):

BE265181 BU660755 BC008296 BM456170 CR600819 AB018323 AI341811 AI923971 
AA719275 CD368911 BU079145 BG203616 AA465547 CA952644 AJ278544 BX330147 
R25177 BQ694638 AW835673 BG207259 BC053678 BG181379 BG191276 AV645419 

Unigene Cluster for KDM4C:

Lysine (K)-specific demethylase 4C
Hs.709425  [show with all ESTs]
Unigene Representative Sequence: NM_015061


GeneLoc Exon Structure

3 Ensembl transcripts including schematic representations:
ENST00000381306  ENST00000401787  ENST00000381309  
(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

KDM4C expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for KDM4C

1 / 2

11 probe-sets matching KDM4C gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
76254_at2 U95-E 1 1.00 1.00 0.51 1.25 -- -- -- -- --

57978_at2 U95-B 1 1.00 1.00 0.42 0.34 -- -- -- -- --

34979_at2 U95-A 1 1.00 1.00 0.45 0.12 -- -- -- -- --

69042_at2 U95-D 1 1.00 1.00 0.64 0.60 -- -- -- -- --
60153_at2 U95-C 1 1.00 1.00 0.51 1.19 -- -- -- -- --
79538_f_at2 U95-E 1 0.81 1.00 0.33 1.01 -- -- -- -- --

209984_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

214861_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

209984_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

1556493_a_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

214861_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  KDM4C for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: ATTTTTCTTT

SOURCE GeneReport for Unigene cluster: Hs.709425

UniProtKB/Swiss-Prot: KDM4C_HUMAN, Q9H3R0
Tissue specificity: Overexpressed in several esophageal squamous cell carcinomas (ESCs)

(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 KDM4C gene from 5/7 species (see all 7 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
JMJD2C1   -- jumonji domain containing 2C 89.65(n)
90.12(a)
474704  XM_531930.2  XP_531930.2 
chimpanzee
(Pan troglodytes)
JMJD2C1   -- jumonji domain containing 2C 99.08(n)
99.34(a)
464989  XM_001144352.1  XP_001144352.1 
rat
(Rattus norvegicus)
Jmjd2c1   -- jumonji domain containing 2C 83.41(n)
83.75(a)
298144  XM_216426.4  XP_216426.4 
mouse
(Mus musculus)
Kdm4c5
Jmjd2c1
45
lysine (K)-specific demethylase 4C5
jumonji domain containing 2C1
84.09(n)1
84.72(a)1
768041  NM_144787.11  NP_659036.11 
 AA5174675  AI1186795  (see all 18)
baker's yeast
(Saccharomyces cerevisiae)
RPH1(YER169W)4 5(523364-525754) JmjC domain-containing histone demethylase which can more   -- 856916  NP_011096.1 
About this table        Species with no ortholog for KDM4C

ENSEMBL Gene Tree for KDM4C
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for KDM4C gene
KDM4D2  KDM4A2  JARID22  KDM4B2  

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


10/2890 NCBI SNPs in KDM4C are shown (see all 2890 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 1205)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 9 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs9135901,2
A,C,F,H,O7164898(+) TACACA/CCAATG 1 -- ut31 ese312Minor allele frequency- C:0.40MN NA EU EA WA 1162
rs9135881,2
A,C,F,H,O7164673(+) ACCCTG/ATATAC 1 I/V mis1 ese325Minor allele frequency- A:0.34NA EA MN EU WA 2276
rs9135891,2
A,C,F,H,O7164773(+) TGGAAA/GAGAGA 1 -- ut31 trp320Minor allele frequency- G:0.40NA EA MN EU WA 3248
rs9439251,2
A,C,F,H7165689(+) AACCAA/GTAGAA 1 -- ng314Minor allele frequency- G:0.15EU EA WA 354
rs70459561,2
A,C,F,H7165734(+) TACTGC/TGGCCC 1 -- ng315Minor allele frequency- T:0.11NA EU WA 374
rs47422591,2
A,C,F,H6745968(+) AGGTTC/AGTATA 1 -- ng518Minor allele frequency- A:0.44EU EA WA 838
rs47422601,2
A,C,F,H6747031(+) CTCTGT/CAGGAA 1 -- ng514Minor allele frequency- C:0.45EU EA WA 416
rs28209341,2
A,C,F,H7166125(-) GCTTTC/TTGCTG 1 -- ng314Minor allele frequency- T:0.28EU EA WA 410
rs22960671,2
C,F,H,O6974236(+) AAGTCA/GATGGG 1 D/N mis114Minor allele frequency- N:0.00EA NA EU WA 2618
rs14172901,2
A,C,F,H7036917(+) CAATAA/GGTAAG 1 K/R mis117Minor allele frequency- G:0.09NS NA EU EA WA 1166
About this table

HapMap Linkage Disequilibrium images for KDM4C (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 605469

2 Novoseek disease relationships for KDM4C gene

Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
carcinoma squamous cell 42.05 7 16732293 (2), 15138608 (1), 11346465 (1)
cancer 0.00 1 16732293 (1)
About this table

(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

10/17 PubMed articles for KDM4C gene (see all 17 ):
(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: 23081 HGNC: 17071 AceView: JMJD2C Ensembl:ENSG00000107077 euGenes: HUgn23081
ECgene: KDM4C H-InvDB: KDM4C
(According to HUGE)
About This Section

HUGE: KIAA0780
(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

NameDescription
ATLAS Chromosomes in Cancer entry for KDM4C Genetics and Cytogenetics in Oncology and Haematology
(Available from WIS Yeda, Salk, Tufts)
About This Section

  --
(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 KDM4C:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



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