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JADE3 Gene

protein-coding   GIFtS: 44
GCID: GC0XP046773

Jade Family PHD Finger 3

(Previous name: PHD finger protein 16)
(Previous symbol: PHF16)
  Search for JADE3
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
Jade Family PHD Finger 31 2     KIAA02153 5
PHF161 2 3 5     JADE-32
PHD Finger Protein 161 2 3     Protein Jade-32
Jade Family PHD Finger Protein 32 3     

External Ids:    HGNC: 229821   Entrez Gene: 97672   Ensembl: ENSG000001022217   OMIM: 3006185   UniProtKB: Q926133   

Export aliases for JADE3 gene to outside databases


(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 JADE3 Gene:
This gene encodes a member of a family of large proteins containing PHD (plant homeo domain)-type zinc fingers.
The encoded protein may be associated in a nuclear complex that functions in histone H4 acetylation. Alternative
splicing results in multiple transcript variants encoding the same protein. (provided by RefSeq, Aug 2013)

GeneCards Summary for JADE3 Gene:
JADE3 (jade family PHD finger 3) is a protein-coding gene. An important paralog of this gene is JADE2.

UniProtKB/Swiss-Prot: JADE3_HUMAN, Q92613
Function: Component of the HBO1 complex which has a histone H4-specific acetyltransferase activity, a reduced
activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo

Gene Wiki entry for JADE3 (PHF16) 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  NC_018934.2  NT_079573.5  
Regulatory elements:
   Search for regulatory transcription factor binding sites for JADE3
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidJADE3 promoter sequence
   Search Chromatin IP Primers for JADE3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat JADE3


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

Entrez Gene cytogenetic band: Xp11.23   Ensembl cytogenetic band:  Xp11.23   HGNC cytogenetic band: Xp11.3

JADE3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
JADE3 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP046773:  view genomic region     (about GC identifiers)

Start:
46,771,711 bp from pter      End:
46,920,641 bp from pter
Size:
148,931 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: JADE3_HUMAN, Q92613 (See protein sequence)
Recommended Name: Protein Jade-3  
Size: 823 amino acids; 93808 Da
Subunit: Component of the HBO1 complex composed at least of ING4 or ING5, KAT7/HBO1, MEAF6, and one of JADE1,
JADE2 and JADE3
Sequence caution: Sequence=BAA13205.2; Type=Erroneous initiation;
Secondary accessions: Q6IE79

Explore the universe of human proteins at neXtProt for JADE3: NX_Q92613

Explore proteomics data for JADE3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See JADE3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001070913.1  NP_055550.1  

    ENSEMBL proteins: 
     ENSP00000391009   ENSP00000218343   ENSP00000400584   ENSP00000380373  
    Reactome Protein details: Q92613

    JADE3 Human Recombinant Protein Products:

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    Browse CLIAs at Cloud-Clone Corp.


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

    Selected InterPro protein domains (see all 6):
     IPR001965 Znf_PHD
     IPR013083 Znf_RING/FYVE/PHD
     IPR019786 Zinc_finger_PHD-type_CS
     IPR011011 Znf_FYVE_PHD
     IPR019542 Enhancer_polycomb-like_N

    Graphical View of Domain Structure for InterPro Entry Q92613

    ProtoNet protein and cluster: Q92613

    UniProtKB/Swiss-Prot: JADE3_HUMAN, Q92613
    Similarity: Belongs to the JADE family
    Similarity: Contains 1 PHD-type zinc finger


    JADE3 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: JADE3_HUMAN, Q92613
    Function: Component of the HBO1 complex which has a histone H4-specific acetyltransferase activity, a reduced
    activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo
    Induction: By estradiol in estrogen-responsive breast cancer cells

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    JADE3 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for JADE3:
     Synthetic lethal with Ras 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Phf16):
     normal 

    JADE3 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for JADE3
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    miRNA
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    miRTarBase miRNAs that target JADE3:
    hsa-mir-484 (MIRT041807), hsa-mir-21-5p (MIRT030778), hsa-mir-24-3p (MIRT030405), hsa-mir-7-5p (MIRT025688), hsa-mir-193b-3p (MIRT016334)

    Block miRNA regulation of human, mouse, rat JADE3 using miScript Target Protectors
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000123histone acetyltransferase complex IDA16387653

    JADE3 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 JADE3 About    
    See pathways by source

    SuperPathContained pathways About
    1RNA Polymerase I Promoter Opening
    HATs acetylate histones0.34
    Chromatin organization0.34
    Chromatin modifying enzymes0.34

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for JADE3
        HATs acetylate histones



    JADE3 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for JADE3
    Interactions:

        Search GeneGlobe Interaction Network for JADE3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

    Selected Interacting proteins for JADE3 (Q926133 ENSP000002183434) via UniProtKB, MINT, STRING, and/or I2D (see all 14)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ING4Q9UNL43, ENSP000003800244I2D: score=1 STRING: ENSP00000380024
    KAT7O952513, ENSP000002590214I2D: score=1 STRING: ENSP00000259021
    ING5Q8WYH83, ENSP000003221424I2D: score=1 STRING: ENSP00000322142
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    TCP11ENSP000003087084STRING: ENSP00000308708
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0043966histone H3 acetylation IDA16387653
    GO:0043981histone H4-K5 acetylation IDA16387653
    GO:0043982histone H4-K8 acetylation IDA16387653
    GO:0043983histone H4-K12 acetylation IDA16387653
    GO:0043984NOT histone H4-K16 acetylation IDA16387653

    JADE3 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 JADE3



    (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,
    Conferences by KenesGroup, 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 JADE3 gene (2 alternative transcripts): 
    NM_001077445.2  NM_014735.4  

    Unigene Cluster for JADE3:

    PHD finger protein 16
    Hs.371977  [show with all ESTs]
    Unigene Representative Sequence: D86969
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000424392 ENST00000218343(uc004dgy.3) ENST00000455411 ENST00000397189(uc004dgx.3)

    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat JADE3

    Additional mRNA sequence: 

    AF127774.1 AK291220.1 BC113880.1 BC114487.1 D86969.1 

    4 DOTS entries:

    DT.413585  DT.97838422  DT.121289853  DT.100745292 

    1 AceView cDNA sequence:

    AL703879 

    GeneLoc Exon Structure


    (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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    JADE3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    JADE3 Expression
    About this image

    JADE3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    JADE3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.371977

    UniProtKB/Swiss-Prot: JADE3_HUMAN, Q92613
    Tissue specificity: Ubiquitously expressed, with highest levels in placenta and uterus

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for JADE3

    (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.

    Orthologs for JADE3 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Phf165
    Jade31
    PHD finger protein 165
    jade family PHD finger 31
    84.89(n)1
    82.02(a)1
      X (15.90 cM)5
    3822071  NM_199317.11  NP_955021.11 
     204256885 
    chicken
    (Gallus gallus)
    Aves PHF161 PHD finger protein 16 75.05(n)
    74.48(a)
      418674  XM_004938456.1  XP_004938513.1 
    lizard
    (Anolis carolinensis)
    Reptilia JADE36
    jade family PHD finger 3
    73(a)
    1 ↔ 1
    3(112070066-112091310)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.5662 Transcribed sequence with moderate similarity to protein more 77.81(n)    AL864925.2 
    zebrafish
    (Danio rerio)
    Actinopterygii jade32 jade3 protein 77.72(n)   387595  BC045468.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta rno6
    rhinoceros
    10(a)
    1 → many
    3L(187207-199762)


    ENSEMBL Gene Tree for JADE3 (if available)
    TreeFam Gene Tree for JADE3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for JADE3 gene
    JADE22  BRD12  BRPF12  MLLT102  PHF142  JADE12  MLLT62  BRPF32  
    3 SIMAP similar genes for JADE3 using alignment to 3 protein entries:     JADE3_HUMAN (see all proteins):
    JADE1    PHF15    JADE2

    JADE3 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 JADE3 (see all 1703)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1901627601,2
    --44481243(+) TCTACA/GTTAAT 2 -- us2k10--------
    rs1857298661,2
    --46688831(+) GAAATG/TACAAA 1 -- us2k10--------
    rs1126976861,2
    F--46688892(+) AAAGCA/GGTGAC 1 -- us2k11Minor allele frequency- G:0.00CSA 1
    rs1809595801,2
    --46689337(+) GTAAAC/TGAAAA 2 -- us2k10--------
    rs1854335871,2
    --46689801(+) AAGGTC/TTGTTG 2 -- us2k10--------
    rs59062891,2
    C--46689878(+) atataC/Tacaca 2 -- us2k11Minor allele frequency- T:0.00NA 2
    rs1997573501,2
    --46689898(+) TATAT-/ATAC  
            
    ATACA
    2 -- us2k10--------
    rs1390683211,2
    --46689995(+) AAGAAC/TGCGTG 2 -- us2k10--------
    rs1498812191,2
    C--46690045(+) CTTCGA/GAGCTA 2 -- us2k10--------
    rs1909712901,2
    --46690214(+) CTGATA/TGAAAG 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for JADE3 (46771711 - 46920641 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for JADE3: --
    Locus Specific Mutation Databases (LSDB): JADE3

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing JADE3
    DNA2.0 Custom Variant and Variant Library Synthesis for JADE3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300618    OMIM disorders: --


    JADE3 for disorders           About GeneDecksing


    Export disorders for JADE3 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 JADE3 gene, integrated from 10 sources (see all 24):
    (articles sorted by number of sources associating them with JADE3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. (PubMed id 16387653)1, 2 Doyon Y.... Cote J. (Mol. Cell 2006)
    2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Identification of Jade1, a gene encoding a PHD zinc finger protein, in a gene trap mutagenesis screen for genes involved in anteroposterior axis development. (PubMed id 14612400)1, 2 Tzouanacou E.... Wilson V. (Mol. Cell. Biol. 2003)
    6. An integrated, functionally annotated gene map of the DXS8026-ELK1 interval on human Xp11.3-Xp11.23: potential hotspot for neurogenetic disorders. (PubMed id 11944989)1, 3 Thiselton D.L.... Meindl A. (Genomics 2002)
    7. Identification of human estrogen-inducible transcripts that potentially mediate the apoptotic response in breast cancer. (PubMed id 10775800)1, 2 Szelei J....Sonnenschein C. (J. Steroid Biochem. Mol. Biol. 2000)
    8. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PubMed id 9039502)1, 2 Nagase T.... Nomura N. (DNA Res. 1996)
    9. Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach. (PubMed id 23281010)1 Li X....Kapoor T.M. (Protein Sci. 2013)
    10. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (Nat. Methods 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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, Kegg, and/or H-InvDB)
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    Entrez Gene: 9767 HGNC: 22982 AceView: PHF16 Ensembl:ENSG00000102221 euGenes: HUgn9767
    ECgene: JADE3 H-InvDB: JADE3

    (According to HUGE)
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    HUGE: KIAA0215

    (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 JADE3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for JADE3 gene:
    Search GeneIP for patents involving JADE3

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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