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KDM5C Gene

protein-coding   GIFtS: 59
GCID: GC0XM053220

Lysine (K)-Specific Demethylase 5C

(Previous names: Jumonji, AT rich interactive domain 1C (RBP2-like), Smcy...)
(Previous symbols: SMCX, JARID1C, MRX13)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Lysine (K)-Specific Demethylase 5C1 2     Jumonji, AT Rich Interactive Domain 1C1
JARID1C1 2 3 5     Smcy Homolog, X-Linked (Mouse)1
SMCX1 2 3 5     MRXJ2
DXS1272E2 3 5     MRXSJ2
XE1692 3 5     JmjC Domain-Containing Protein SMCX2
MRX131 2     Lysine-Specific Demethylase 5C2
Jumonji, AT Rich Interactive Domain 1C (RBP2-Like)1 2     Selected CDNA On X2
Mental Retardation, X-Linked 131 2     Smcx Homolog, X Chromosome2
Histone Demethylase JARID1C2 3     Smcy Homolog, X-Linked2
Protein SmcX2 3     EC 1.14.11.-3
Jumonji/ARID Domain-Containing Protein 1C2 3     Protein Xe1693
MRXSCJ2 5     EC 1.14.118

External Ids:    HGNC: 111141   Entrez Gene: 82422   Ensembl: ENSG000001260127   OMIM: 3146905   UniProtKB: P412293   

Export aliases for KDM5C gene to outside databases

Previous GC identifers: GC0XM053237 GC0XM050285


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for KDM5C Gene:
This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one
JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the
regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked
mental retardation. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Apr 2009)

GeneCards Summary for KDM5C Gene:
KDM5C (lysine (K)-specific demethylase 5C) is a protein-coding gene. Diseases associated with KDM5C include x-linked syndromic mental retardation, claes-jensen type, and hemiplegia. GO annotations related to this gene include oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors and histone demethylase activity (H3-K4 specific). An important paralog of this gene is JARID2.

UniProtKB/Swiss-Prot: KDM5C_HUMAN, P41229
Function: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role
in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'.
Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional
repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements

Gene Wiki entry for KDM5C (JARID1C) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000023.11  NT_011630.15  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the KDM5C gene promoter:
         TBP   RP58   HTF   GATA-2   CREB   Ik-2   HOXA5   deltaCREB   NF-E2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKDM5C promoter sequence
   Search Chromatin IP Primers for KDM5C

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM5C


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xp11.22-p11.21   Ensembl cytogenetic band:  Xp11.22   HGNC cytogenetic band: Xp11.22-p11.21

KDM5C Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KDM5C gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM053220:  view genomic region     (about GC identifiers)

Start:
53,220,503 bp from pter      End:
53,254,604 bp from pter
Size:
34,102 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: KDM5C_HUMAN, P41229 (See protein sequence)
Recommended Name: Lysine-specific demethylase 5C  
Size: 1560 amino acids; 175720 Da
Cofactor: Alpha-ketoglutarate
Cofactor: Binds 1 Fe(2+) ion per subunit
Subunit: Part of two distinct complexes, one containing E2F6, and the other containing REST
Miscellaneous: Escapes X-inactivation
1 PDB 3D structure from and Proteopedia for KDM5C:
2JRZ (3D)    
Secondary accessions: B0QZ44 B4E3I2 F5H3T1 Q5JUX3 Q5JUX4 Q5JUX5 Q7Z5S5
Alternative splicing: 5 isoforms:  P41229-1   P41229-2   P41229-3   P41229-4   P41229-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for KDM5C: NX_P41229

Explore proteomics data for KDM5C at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys91, Lys101, Lys377, Lys739, Lys776, Lys1114, Lys1121
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for KDM5C (P41229) (see all 61)
     DKEYKPH  STKRSRW  LLEVLCP  TFLKKNS 


    See KDM5C Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001140174.1  NP_001269551.1  NP_004178.2  

    ENSEMBL proteins: 
     ENSP00000364550   ENSP00000385394   ENSP00000364528   ENSP00000364532   ENSP00000409757  
     ENSP00000407277   ENSP00000344004   ENSP00000445176  

    KDM5C Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for KDM5C

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    Cloud-Clone Corp. CLIAs for KDM5C


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    KDM: Chromatin-modifying enzymes / K-demethylases
    PHF: Zinc fingers, PHD-type

    Selected InterPro protein domains (see all 10):
     IPR001965 Znf_PHD
     IPR013083 Znf_RING/FYVE/PHD
     IPR003347 JmjC_dom
     IPR013637 Lys_sp_deMease_like_dom
     IPR019786 Zinc_finger_PHD-type_CS

    Graphical View of Domain Structure for InterPro Entry P41229

    ProtoNet protein and cluster: P41229

    Selected Blocks protein domains (see all 6):
    IPB001606 ARID (AT-rich interaction domain) protein
    IPB001965 Zn-finger-like
    IPB003347 Transcription factor jumonji
    IPB003349 Transcription factor jumonji
    IPB004198 Zn-finger


    UniProtKB/Swiss-Prot: KDM5C_HUMAN, P41229
    Domain: The first PHD-type zinc finger domain recognizes and binds H3-K9Me3
    Domain: Both the JmjC domain and the JmjN domain are required for enzymatic activity
    Similarity: Belongs to the JARID1 histone demethylase family
    Similarity: Contains 1 ARID domain
    Similarity: Contains 1 JmjC domain
    Similarity: Contains 1 JmjN domain
    Similarity: Contains 2 PHD-type zinc fingers


    KDM5C for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: KDM5C_HUMAN, P41229
    Function: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role
    in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'.
    Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional
    repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements

         Enzyme Numbers (IUBMB): EC 1.14.11.-1 EC 1.14.112

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IEA--
    GO:0032453histone demethylase activity (H3-K4 specific) IDA17320160
         
    KDM5C for ontologies           About GeneDecksing


    Phenotypes:
         4 GenomeRNAi human phenotypes for KDM5C:
     Decreased BPV1 E2 protein expr  Decreased POU5F1-GFP protein e  Increased HPV18 LCR reporter a  Increased cell death in HCC-19 

         3 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Kdm5c):
     cardiovascular system  embryogenesis  normal 

    KDM5C for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KDM5C
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for KDM5C
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for KDM5C

    miRNA
    Products:
        
    miRTarBase miRNAs that target KDM5C:
    hsa-mir-26a-5p (MIRT050192), hsa-mir-484 (MIRT041792), hsa-mir-605-5p (MIRT040478), hsa-mir-1229-3p (MIRT036342), hsa-mir-324-3p (MIRT042989), hsa-mir-378a-3p (MIRT043887), hsa-mir-320a (MIRT044496), hsa-mir-425-3p (MIRT042424)

    Block miRNA regulation of human, mouse, rat KDM5C using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM5C (see all 71):
    hsa-miR-193a-3p hsa-miR-578 hsa-miR-3916 hsa-miR-1304 hsa-miR-4325 hsa-miR-3150b-3p hsa-miR-3613-3p hsa-miR-556-3p
    SwitchGear 3'UTR luciferase reporter plasmidKDM5C 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for KDM5C
    Predesigned siRNA for gene silencing in human, mouse, rat KDM5C

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector (see all 2): KDM5C (NM_004187)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for KDM5C
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM5C

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM5C


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    KDM5C_HUMAN, P41229: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IDA18078810

    KDM5C for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for KDM5C About    
    See pathways by source

    SuperPathContained pathways About
    1Chromatin Regulation / Acetylation
    Chromatin Regulation / Acetylation

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for KDM5C
        Chromatin Regulation / Acetylation



    KDM5C for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including KDM5C: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for KDM5C

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for KDM5C (P412293 ENSP000003645504) via UniProtKB, MINT, STRING, and/or I2D (see all 120)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4BP628053, ENSP000003665814I2D: score=4 STRING: ENSP00000366581
    HIST1H4CP628053, ENSP000003670344I2D: score=4 STRING: ENSP00000367034
    HIST1H4DP628053, ENSP000003432824I2D: score=4 STRING: ENSP00000343282
    HIST1H4EP628053, ENSP000003536244I2D: score=4 STRING: ENSP00000353624
    HIST1H4HP628053, ENSP000002893524I2D: score=4 STRING: ENSP00000289352
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0034720histone H3-K4 demethylation IDA17320160
    GO:0055114oxidation-reduction process ----

    KDM5C for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for KDM5C



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for KDM5C gene (3 alternative transcripts): 
    NM_001146702.1  NM_001282622.1  NM_004187.3  

    Unigene Cluster for KDM5C:

    Lysine (K)-specific demethylase 5C
    Hs.631768  [show with all ESTs]
    Unigene Representative Sequence: NM_004187
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000375401 ENST00000404049 ENST00000375379 ENST00000375383 ENST00000477109
    ENST00000497100 ENST00000465402 ENST00000481369 ENST00000497995 ENST00000429877
    ENST00000495519 ENST00000467093 ENST00000428012 ENST00000349663 ENST00000452825(uc004drz.3 uc022bxe.1 uc004dsa.3)

    miRNA
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    Block miRNA regulation of human, mouse, rat KDM5C using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM5C (see all 71):
    hsa-miR-193a-3p hsa-miR-578 hsa-miR-3916 hsa-miR-1304 hsa-miR-4325 hsa-miR-3150b-3p hsa-miR-3613-3p hsa-miR-556-3p
    SwitchGear 3'UTR luciferase reporter plasmidKDM5C 3' UTR sequence
    Inhib. RNA
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): KDM5C (NM_004187)
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat KDM5C
      QuantiFast Probe-based Assays in human, mouse, rat KDM5C

    Additional mRNA sequence: 

    AF069136.1 AK304732.1 AK308077.1 AY927525.1 AY927613.1 AY927614.1 BC054499.2 EF613277.1 
    L25270.1 Z29650.1 

    15 DOTS entries:

    DT.314594  DT.100817390  DT.92428580  DT.95195172  DT.86857392  DT.100817379  DT.121298854  DT.95249943 
    DT.100817387  DT.100817394  DT.100840162  DT.121298874  DT.87012280  DT.100817385  DT.100830833 

    Selected AceView cDNA sequences (see all 327):

    AI858456 CF890786 AA348318 BM977359 BU633909 CB243084 BM785022 BU681761 
    CA944929 BM983446 BM744459 BX493253 BU947654 BU153721 AW016007 AA725213 
    AA358508 BM467977 AV653156 AI264498 BF095232 BX110463 L25270 BQ070750 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM5C (see all 12)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^
    SP1:                          -     -     -     -           -     -                                                     -                                       
    SP2:                          -     -     -     -           -     -                                                     -                                       
    SP3:                          -                 -           -     -                                                                                             
    SP4:                                                        -     -                                                                                             
    SP5:                                                                                                                                                            

    ExUns: 16a · 16b ^ 17 ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25a · 25b · 25c ^ 26a · 26b ^ 27 ^ 28
    SP1:                          -                       -                                                                                 
    SP2:                          -                       -                                                                                 
    SP3:                                                                                                                                    
    SP4:                                                                                                                                    
    SP5:                                                                                -                                                   


    ECgene alternative splicing isoforms for KDM5C

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    KDM5C expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGTAATAAA
    KDM5C Expression
    About this image

    KDM5C Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM5C Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631768

    UniProtKB/Swiss-Prot: KDM5C_HUMAN, P41229
    Tissue specificity: Expressed in all tissues examined. Highest levels found in brain and skeletal muscle

        Pathway & Disease-focused RT2 Profiler PCR Array including KDM5C: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

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    (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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for KDM5C gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm5c1 , 5 lysine (K)-specific demethylase 5C1, 5 90.22(n)1
    95.52(a)1
      X (68.46 cM)5
    205911  NM_013668.31  NP_038696.21 
     1522330205 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    80(a)
    1 → many
    1(204862436-204882164)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ066924.12   -- 76.41(n)    BJ066924.1 
    zebrafish
    (Danio rerio)
    Actinopterygii kdm5c1 lysine (K)-specific demethylase 5C 65.82(n)
    69.16(a)
      553406  NM_001123234.1  NP_001116706.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta lid6
    little imaginal discs
    35(a)
    1 → many
    2L(5989463-5999501)
    worm
    (Caenorhabditis elegans)
    Secernentea rbr-26
    Protein RBR-2 (rbr-2) mRNA, complete cds
    27(a)
    1 → many
    IV(10920107-10926797) WBGene00004319
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes JHD2(YJR119C)4 JmjC domain family histone demethylase specific for more   --   10(646490-644304) 853583  NP_012653.1 
    rice
    (Oryza sativa)
    Liliopsida Os.71302 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 80.36(n)    AK073475.1 


    ENSEMBL Gene Tree for KDM5C (if available)
    TreeFam Gene Tree for KDM5C (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM5C gene
    JARID22  KDM5B2  KDM5A2  KDM5D2  
    9 SIMAP similar genes for KDM5C using alignment to 5 protein entries:     KDM5C_HUMAN (see all proteins):
    JARID1C    KDM5D    PLU-1    KDM5A    KDM5B    JARID2
    JARID1B    DKFZp434N0335    DKFZp434D0815

    KDM5C for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for KDM5C (see all 545)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0329874
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0329872 S R mis40--------
    VAR_0227324
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0227322 E K mis40--------
    VAR_0227304
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0227302 A P mis40--------
    VAR_0227314
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0227312 D Y mis40--------
    VAR_0329884
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0329882 F L mis40--------
    VAR_0227334
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0227332 L F mis40--------
    VAR_0329894
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0329892 R W mis40--------
    VAR_0329864
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0329862 D G mis40--------
    VAR_0329904
    Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)4--see VAR_0329902 Y C mis40--------
    rs1994222381,2
    Cpathogenic153242233(-) AGGTTC/TGGGCT 4 R W mis10--------

    HapMap Linkage Disequilibrium report for KDM5C (53220503 - 53254604 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for KDM5C:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2740175CNV Deletion23290073
    nsv435891CNV Deletion17901297

    Human Gene Mutation Database (HGMD): KDM5C
    Locus Specific Mutation Databases (LSDB): KDM5C

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 314690   
    OMIM disorders: 300534  
    UniProtKB/Swiss-Prot: KDM5C_HUMAN, P41229
  • Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ) [MIM:300534]: A disorder
    characterized by significantly below average general intellectual functioning associated with impairments in
    adaptive behavior and manifested during the developmental period. MRXSCJ patients manifest mental retardation
    associated with variable features such as slowly progressive spastic paraplegia, seizures, facial dysmorphism.
    Note=The disease is caused by mutations affecting the gene represented in this entry

  • 13 diseases for KDM5C:    
    About MalaCards
    x-linked syndromic mental retardation, claes-jensen type    hemiplegia    mental retardation    intellectual disability
    autism spectrum disorder    mental retardation, x-linked    short stature    paraplegia
    spasticity    retinoblastoma    multiple myeloma    myeloma
    neuronitis

    1 disease from the University of Copenhagen DISEASES database for KDM5C:
    Intellectual disability

    KDM5C for disorders           About GeneDecksing

    1 Novoseek inferred disease relationship for KDM5C gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    mental retardation 59.6 6 18697827 (4), 16538222 (1), 15586325 (1)

    Genetic Association Database (GAD): KDM5C

    Export disorders for KDM5C gene to outside databases

    (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)
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    PubMed articles for KDM5C gene, integrated from 10 sources (see all 51):
    (articles sorted by number of sources associating them with KDM5C)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of XE169, a novel human gene that escapes X-inactivation. (PubMed id 8162017)1, 2, 3, 9 Wu J.... Shapiro L.J. (Hum. Mol. Genet. 1994)
    2. A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human. (PubMed id 7951230)1, 2, 3 Agulnik A.I.... Bishop C.E. (Hum. Mol. Genet. 1994)
    3. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. (PubMed id 15586325)1, 2, 9 Jensen L.R.... Lenzner S. (Am. J. Hum. Genet. 2005)
    4. Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype-phenotype correlation. (PubMed id 19826449)1, 3, 9 Rujirabanjerd S....Gecz J. (Eur. J. Hum. Genet. 2010)
    5. A novel mutation in JARID1C gene associated with mental retardation. (PubMed id 16538222)1, 2, 9 Santos C....Mila M. (Eur. J. Hum. Genet. 2006)
    6. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. (PubMed id 17320161)1, 2 Christensen J.... Helin K. (Cell 2007)
    7. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. (PubMed id 17468742)1, 2 Tahiliani M.... Shi Y. (Nature 2007)
    8. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. (PubMed id 17320160)1, 2 Iwase S.... Shi Y. (Cell 2007)
    9. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (Nat. Biotechnol. 2006)
    10. Novel JARID1C/SMCX mutations in patients with X-linked mental retardation. (PubMed id 16541399)1, 2 Tzschach A.... Jensen L.R. (Hum. Mutat. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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, Kegg, and/or H-InvDB)
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    Entrez Gene: 8242 HGNC: 11114 AceView: JARID1C Ensembl:ENSG00000126012 euGenes: HUgn8242
    ECgene: KDM5C H-InvDB: KDM5C

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for KDM5C Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=JARID1C[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KDM5C gene:
    Search GeneIP for patents involving KDM5C

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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