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KDM5A Gene

protein-coding   GIFtS: 53
GCID: GC12M000389

Lysine (K)-Specific Demethylase 5A

(Previous names: retinoblastoma-binding protein 2, Jumonji, AT rich interactive...)
(Previous symbols: RBBP2, JARID1A)
  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 5A1 2     Jumonji, AT Rich Interactive Domain 1A1
RBBP21 2 3 5     Jumonji, AT Rich Interactive Domain 1A (RBBP2-Like)1
JARID1A1 3 5     Jumonji, AT Rich Interactive Domain 1A (RBP2-Like)2
RBP22 3 5     Lysine-Specific Demethylase 5A2
Retinoblastoma-Binding Protein 21 3     Retinoblastoma Binding Protein 22
Histone Demethylase JARID1A2 3     EC 1.14.11.-3
Jumonji/ARID Domain-Containing Protein 1A2 3     EC 1.14.118
RBBP-22 3     

External Ids:    HGNC: 98861   Entrez Gene: 59272   Ensembl: ENSG000000736147   OMIM: 1802025   UniProtKB: P293753   

Export aliases for KDM5A gene to outside databases

Previous GC identifer: GC12M000259


(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 KDM5A Gene:
This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein
family. The encoded protein plays a role in gene regulation through the histone code by specifically
demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including
retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene
may play a role in tumor progression. (provided by RefSeq, Aug 2013)

GeneCards Summary for KDM5A Gene:
KDM5A (lysine (K)-specific demethylase 5A) is a protein-coding gene. Diseases associated with KDM5A include retinoblastoma, and spondylitis. 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 sequence-specific DNA binding transcription factor activity. An important paralog of this gene is KDM5C.

UniProtKB/Swiss-Prot: KDM5A_HUMAN, P29375
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'. May stimulate transcription
mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell
differentiation. May participate in transcriptional repression of cytokines such as CXCL12

Gene Wiki entry for KDM5A (JARID1A) 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_000012.12  NC_018923.2  NT_009759.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the KDM5A gene promoter:
         Pax-2   Pax-2a   STAT5A   C/EBPalpha   HNF-1A   E2F   Pax-2b   E2F-1   HNF-1   FOXO4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKDM5A promoter sequence
   Search Chromatin IP Primers for KDM5A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM5A


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

Entrez Gene cytogenetic band: 12p11   Ensembl cytogenetic band:  12p13.33   HGNC cytogenetic band: 12p13.33

KDM5A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KDM5A gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M000389:  view genomic region     (about GC identifiers)

Start:
389,223 bp from pter      End:
498,620 bp from pter
Size:
109,398 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: KDM5A_HUMAN, P29375 (See protein sequence)
Recommended Name: Lysine-specific demethylase 5A  
Size: 1690 amino acids; 192095 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subunit: Interacts with SUZ12; the interaction is direct (By similarity). Interacts with the viral protein-binding
domain of RB1. Interacts with ESR1, MYC, MYCN and LMO2
Sequence caution: Sequence=AAB28544.1; Type=Frameshift; Positions=Several; Sequence=BAE06081.1; Type=Erroneous
initiation;
4 PDB 3D structures from and Proteopedia for KDM5A:
2JXJ (3D)        2KGG (3D)        2KGI (3D)        3GL6 (3D)    
Secondary accessions: A8MV76 Q4LE72 Q86XZ1
Alternative splicing: 2 isoforms:  P29375-1   P29375-2   

Explore the universe of human proteins at neXtProt for KDM5A: NX_P29375

Explore proteomics data for KDM5A at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys347, Lys392, Lys425, Lys733, Lys1275
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for KDM5A (P29375) (see all 20)
     GEPKTWY  ERWEEKA  YSINYLH  TTCFLSA 


    See KDM5A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001036068.1  
    ENSEMBL proteins: 
     ENSP00000382688   ENSP00000440622   ENSP00000443854   ENSP00000438203   ENSP00000444251  
     ENSP00000372265  

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    (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 P29375

    ProtoNet protein and cluster: P29375

    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: KDM5A_HUMAN, P29375
    Domain: The GSGFP motif is required for the interaction with SUZ12 (By similarity)
    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 3 PHD-type zinc fingers


    KDM5A 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: KDM5A_HUMAN, P29375
    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'. May stimulate transcription
    mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell
    differentiation. May participate in transcriptional repression of cytokines such as CXCL12

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

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003682chromatin binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS8414517
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    KDM5A for ontologies           About GeneDecksing


    Phenotypes:
         9 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Kdm5a):
     behavior/neurological  cellular  endocrine/exocrine gland  growth/size/body  hematopoietic system 
     immune system  mortality/aging  normal  tumorigenesis 

    KDM5A for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Kdm5atm1.1Kael for KDM5A

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KDM5A
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for KDM5A

    miRNA
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    miRTarBase miRNAs that target KDM5A:
    hsa-mir-335-5p (MIRT017637)

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    Selected qRT-PCR Assays for microRNAs that regulate KDM5A (see all 98):
    hsa-miR-582-3p hsa-miR-548j hsa-miR-607 hsa-miR-199a-3p hsa-miR-134 hsa-miR-3916 hsa-miR-409-5p hsa-miR-3116
    SwitchGear 3'UTR luciferase reporter plasmidKDM5A 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for KDM5A
    Predesigned siRNA for gene silencing in human, mouse, rat KDM5A

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector: KDM5A (NM_001042603)
    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM5A


    (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
    KDM5A_HUMAN, P29375: Nucleus, nucleolus. Note=Occupies promoters of genes involved in RNA metabolism and
    mitochondrial function (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IEA--
    GO:0005737cytoplasm IDA--
    GO:0019907colocalizes with cyclin-dependent protein kinase activating kinase holoenzyme complex IDA11445587

    KDM5A 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 KDM5A About    
    See pathways by source

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

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for KDM5A
        Visual Cycle in Retinal Rods

    1 Cell Signaling Technology (CST) Pathway for KDM5A
        Chromatin Regulation / Acetylation



    KDM5A for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KDM5A
    Interactions:

        GeneGlobe Interaction Network for KDM5A

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

    Selected Interacting proteins for KDM5A (P293753 ENSP000003826884) via UniProtKB, MINT, STRING, and/or I2D (see all 94)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST2H3AQ71DI33, ENSP000003854794I2D: score=1 STRING: ENSP00000385479
    HIST2H3CQ71DI33I2D: score=1 
    HIST2H3DQ71DI33I2D: score=1 
    NR3C1P041503, ENSP000002315094I2D: score=4 STRING: ENSP00000231509
    RARAP102763, ENSP000002540664I2D: score=4 STRING: ENSP00000254066
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006366transcription from RNA polymerase II promoter TAS8414517
    GO:0007275multicellular organismal development IEA--
    GO:0016568chromatin modification IEA--
    GO:0045893positive regulation of transcription, DNA-templated IDA11358960
    GO:0055114oxidation-reduction process ----

    KDM5A 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 KDM5A



    (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 KDM5A gene (2 alternative transcripts): 
    NM_001042603.2  NM_005056.2  

    Unigene Cluster for KDM5A:

    Lysine (K)-specific demethylase 5A
    Hs.76272  [show with all ESTs]
    Unigene Representative Sequence: NM_001042603
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000399788(uc021qsr.1 uc001qif.1) ENST00000540838 ENST00000540156
    ENST00000544760 ENST00000535269 ENST00000541335 ENST00000540168 ENST00000544777
    ENST00000535014 ENST00000536014 ENST00000543507 ENST00000382815(uc010sdn.1 uc010sdo.1)

    miRNA
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    Block miRNA regulation of human, mouse, rat KDM5A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM5A (see all 98):
    hsa-miR-582-3p hsa-miR-548j hsa-miR-607 hsa-miR-199a-3p hsa-miR-134 hsa-miR-3916 hsa-miR-409-5p hsa-miR-3116
    SwitchGear 3'UTR luciferase reporter plasmidKDM5A 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat KDM5A
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    GenScript: all cDNA clones in your preferred vector: KDM5A (NM_001042603)
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      QuantiTect SYBR Green Assays in human, mouse, rat KDM5A
      QuantiFast Probe-based Assays in human, mouse, rat KDM5A

    Additional mRNA sequence: 

    AB209999.1 AF007135.1 AK057703.1 AK225060.1 AK301150.1 AK301273.1 AK307580.1 AK307689.1 
    AL133026.1 BC048307.1 BC053893.1 BC110916.1 S66431.1 

    15 DOTS entries:

    DT.100780845  DT.87016210  DT.75163122  DT.92044835  DT.110527  DT.100780847  DT.100727224  DT.431815 
    DT.95331495  DT.121126262  DT.121126263  DT.121126329  DT.121126345  DT.87000478  DT.97785624 

    Selected AceView cDNA sequences (see all 416):

    AI884688 AA460157 BX092553 BQ285911 AW300068 BQ632303 BQ933481 AW058576 
    AI700672 BM709205 AA469935 BE328608 N80904 AA952997 AA812025 BE301184 
    CA308399 AA906265 AI672662 BC020867 AI146438 BM833997 BC022392 BQ632596 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM5A (see all 7)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a ·
    SP1:                                                                                -                                                                           
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 24b ^ 25 ^ 26 ^ 27a · 27b · 27c ^ 28 ^ 29 ^ 30
    SP1:                                                      
    SP2:                                                      
    SP3:                                                      
    SP4:                                                      
    SP5:                                                      


    ECgene alternative splicing isoforms for KDM5A

    (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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    KDM5A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    KDM5A Expression
    About this image


    KDM5A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Limb (Muscoskeletal System)
             Limb Bud
     
     Testis (Reproductive System)
             Testis Somatic Cells Primitive Gonad
     
     Gonad (Reproductive System)
             Testis Somatic Cells Primitive Gonad
     
     Blood (Hematopoietic System)
             pre Conventional Dendritic Cells Peripheral Blood
     
     Eye (Sensory Organs)
             Corneal Epithelium
    KDM5A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM5A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.76272
        Custom PCR Arrays for KDM5A
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for KDM5A
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    In Situ
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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 animals and fungi.

    Orthologs for KDM5A gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm5a1 , 5 lysine (K)-specific demethylase 5A1, 5 91.74(n)1
    96.69(a)1
      6 (56.95 cM)5
    2148991  NM_145997.21  NP_666109.21 
     1203641245 
    chicken
    (Gallus gallus)
    Aves KDM5A1 lysine (K)-specific demethylase 5A 80.5(n)
    92.18(a)
      418148  XM_004937924.1  XP_004937981.1 
    lizard
    (Anolis carolinensis)
    Reptilia KDM5A6
    lysine (K)-specific demethylase 5A
    91(a)
    1 ↔ 1
    5(11886209-11931909)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ029275.12   -- 78.67(n)    BJ029275.1 
    zebrafish
    (Danio rerio)
    Actinopterygii kdm5a1 lysine (K)-specific demethylase 5A 66.02(n)
    74.44(a)
      100333310  XM_003201640.2  XP_003201688.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta lid1 little imaginal discs 52.58(n)
    49.63(a)
      33837  NM_001258980.1  NP_001245909.1 
    worm
    (Caenorhabditis elegans)
    Secernentea rbr-26
    Protein RBR-2 (rbr-2) mRNA, complete cds
    29(a)
    1 → many
    IV(10920107-10926797) WBGene00004319
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes JHD26
    JmjC domain family histone demethylase specific fo...
    29(a)
    1 → many
    X(644304-646490) YJR119C


    ENSEMBL Gene Tree for KDM5A (if available)
    TreeFam Gene Tree for KDM5A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM5A gene
    KDM5C2  JARID22  KDM5B2  KDM5D2  
    11 SIMAP similar genes for KDM5A using alignment to 6 protein entries:     KDM5A_HUMAN (see all proteins):
    PLU-1    KDM5C    KDM5B    JARID1B    JARID1C    DKFZp434N0335
    KDM5D    DKFZp434D0815    DKFZp434I0617    PHF21A    DKFZp434I2412

    KDM5A 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 KDM5A (see all 2445)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2018219561,2
    Cuntested1495101(+) GAAACA/GAAAGC 2 R C mis10--------
    rs2017299221,2
    C--388744(+) ACTATA/CCNNNN 1 -- ds50010--------
    rs1885711771,2
    --388749(+) ACAGCC/TTCTAT 1 -- ds50010--------
    rs784816201,2
    C,F--388754(+) CTCTAT/CTGTCG 1 -- ds50011Minor allele frequency- C:0.03NA 120
    rs778270141,2
    C,F--388758(+) ATTGTC/TGTCTT 1 -- ds50011Minor allele frequency- T:0.01NA 120
    rs1465547081,2
    --388759(+) TTGTCA/GTCTTT 1 -- ds50010--------
    rs798182341,2
    C,F--388806(+) AAATCA/GTCTAT 1 -- ds50011Minor allele frequency- G:0.02EA 120
    rs1412165411,2
    --388810(+) CATCTA/GTGTCT 1 -- ds50010--------
    rs1449256251,2
    --388865(+) CTTGCA/TTGTGG 1 -- ds50010--------
    rs123179051,2
    C,F,A,H--388877(+) AGGAAG/ACCAAG 1 -- ds500112Minor allele frequency- A:0.23NS EA NA WA CSA 915

    HapMap Linkage Disequilibrium report for KDM5A (389223 - 498620 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for KDM5A (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv34939CNV Loss17911159
    nsv819688CNV Loss19587683
    nsv898564CNV Loss21882294
    nsv570CNV Loss18451855
    esv33025CNV Gain17666407
    nsv898563CNV Gain21882294
    esv33918CNV Gain17666407
    nsv898565CNV Gain21882294
    nsv8883CNV Gain+Loss18304495
    nsv442250CNV CNV18776908

    Human Gene Mutation Database (HGMD): KDM5A
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KDM5A
    DNA2.0 Custom Variant and Variant Library Synthesis for KDM5A

    (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: 180202    OMIM disorders: --

    11 diseases for KDM5A:    
    About MalaCards
    retinoblastoma    spondylitis    ankylosing spondylitis    acute leukemia
    kidney disease    mental retardation    melanoma    leukemia
    thyroiditis    malaria    breast cancer


    KDM5A for disorders           About GeneDecksing

    1 Novoseek inferred disease relationship for KDM5A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoblastoma 76.4 11 10942599 (1), 7935440 (1), 8530100 (1), 16419055 (1) (see all 8)


    Export disorders for KDM5A 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 KDM5A gene, integrated from 10 sources (see all 55):
    (articles sorted by number of sources associating them with KDM5A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of cDNAs for cellular proteins that bind to the retinoblastoma gene product. (PubMed id 1857421)1, 2, 3, 9 Defeo-Jones D.... Oliff A. (Nature 1991)
    2. Retinoblastoma-binding protein 2 (Rbp2) potentiates nuclear hormone receptor-mediated transcription. (PubMed id 11358960)1, 2, 9 Chan S.W. and Hong W. (J. Biol. Chem. 2001)
    3. T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2. (PubMed id 9129143)1, 2, 9 Mao S.... Goorha R.M. (Oncogene 1997)
    4. Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein. (PubMed id 7935440)1, 2, 9 Kim Y.W.... Kaye F.J. (Mol. Cell. Biol. 1994)
    5. 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)
    6. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    7. Binding of pRB to the PHD protein RBP2 promotes cellular differentiation. (PubMed id 15949438)1, 2 Benevolenskaya E.V....Kaelin W.G. Jr. (Mol. Cell 2005)
    8. Characterization of the retinoblastoma binding proteins RBP1 and RBP2. (PubMed id 8414517)1, 2 Fattaey A.R....Jones R.E. (Oncogene 1993)
    9. RBP2 is an MRG15 complex component and down-regulates intragenic histone H3 lysine 4 methylation. (PubMed id 17573780)1, 9 Hayakawa T....Nakayama J. (amp 2007)
    10. Isolation and regional assignment of human chromosome 12p cDNAs. (PubMed id 8530100)1, 9 Baens M....Marynen P. (Genomics 1995)

    (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: 5927 HGNC: 9886 AceView: JARID1AandSLC6A13 Ensembl:ENSG00000073614 euGenes: HUgn5927
    ECgene: KDM5A H-InvDB: KDM5A

    (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 KDM5A Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for KDM5A Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KDM5A gene:
    Search GeneIP for patents involving KDM5A

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



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