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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PHF16 Gene

protein-coding   GIFtS: 50
GCID: GC0XP046771

PHD finger protein 16

 Explore 1 disease affiliated with
PHF16 via our new
 Human Malady Compendium 
Biological research products
for PHF16
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
PHD Finger Protein 161 2 3
KIAA02151 3
JADE32 3
Protein Jade-32

External Ids:    HGNC: 229821   Entrez Gene: 97672   Ensembl: ENSG000001022217   OMIM: 3006185   UniProtKB: Q926133   
ORGUL members:         
NONCODE:n337672    

Export aliases for PHF16 gene to outside databases

Previous GC identifers: GC0XP045598 GC0XP045817 GC0XP046528 GC0XP046656 GC0XP044482


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

Entrez Gene summary for PHF16:
This gene is part of a gene cluster on chromosome Xp11.23. The encoded protein contains a zinc finger motif often found
in transcriptional regulators, however, its exact function is not known. Alternative splicing results in multiple
transcript variants encoding the same protein. (provided by RefSeq, Jul 2008)

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 PHF16


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_079573.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PHF16 gene promoter:
         E2F-3a   E2F-4   E2F-5   E2F   E2F-1   E2F-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPHF16 promoter sequence
   Search SABiosciences Chromatin IP Primers for PHF16

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PHF16


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

PHF16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHF16 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP046771:  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, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

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 PHF15, PHF16 and
PHF17
Sequence caution: Sequence=BAA13205.2; Type=Erroneous initiation;
Secondary accessions: Q6IE79

Explore the universe of human proteins at neXtProt for PHF16: NX_Q92613

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q92613

  • PHF16 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

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

    ENSEMBL proteins: 
     ENSP00000391009   ENSP00000218343   ENSP00000400584   ENSP00000380373  

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    Uscn Proteins for PHF16

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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


    PHF16 for ontologies           About GeneDecksing



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

    PHF16 for domains           About GeneDecksing

    5/6 InterPro domains/families (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


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         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
    Induction: By estradiol in estrogen-responsive breast cancer cells

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    hsa-miR-30c hsa-miR-205 hsa-miR-607 hsa-miR-30d hsa-miR-30a hsa-miR-670 hsa-miR-30b hsa-miR-32*
    SwitchGear 3'UTR luciferase reporter plasmidPHF16 3' UTR sequence
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008270zinc ion binding IEA--


    PHF16 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for PHF16:
     Synthetic lethal with Ras 

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

    PHF16 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PHF16

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for PHF16 (Q926133 ENSP000002183434) via UniProtKB, MINT, STRING, and/or I2D
    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
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    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


    PHF16 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PHF16
    Search CenterWatch for drugs/clinical trials and news about PHF16 / JADE3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PHF16 gene (2 alternative transcripts): 
    NM_001077445.1  NM_014735.3  

    Unigene Cluster for PHF16:

    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)


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    hsa-miR-30c hsa-miR-205 hsa-miR-607 hsa-miR-30d hsa-miR-30a hsa-miR-670 hsa-miR-30b hsa-miR-32*
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    Additional cDNA 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PHF16 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCTTTCAATT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See PHF16 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PHF16

    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
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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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PHF16 gene from 8/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves PHF161 PHD finger protein 16 74.58(n)
    74.58(a)
      418674  XM_416870.3  XP_416870.3 
    lizard
    (Anolis carolinensis)
    Reptilia PHF166
    --
    71(a)
    1 ↔ 1
    3(112070077-112087934)
    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
    6(a)
    1 → many
    3L(187207-199762)
    worm
    (Caenorhabditis elegans)
    Secernentea phf-156
    Protein PHF-15, isoform b
    18(a)
    1 → many
    III(3322961-3331717)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G147406
    RING/FYVE/PHD zinc finger-containing protein
    21(a)
    1 → many
    3(4952004-4953423)
    rice
    (Oryza sativa)
    Liliopsida --
    PHD-finger domain containing protein, putative, ex...
    12(a)
    1 → many
    1(4430532-4432679)


    ENSEMBL Gene Tree for PHF16 (if available)
    TreeFam Gene Tree for PHF16 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PHF16 gene
    PHF172  BRPF12  BRD12  MLLT102  PHF142  PHF152  MLLT62  BRPF32  
    2 SIMAP similar genes for PHF16 using alignment to 3 protein entries:     JADE3_HUMAN (see all proteins):
    PHF17    PHF15

    PHF16 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1379 NCBI SNPs in PHF16 are shown (see all 1379    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1857298661,2
    --46769796(+) GAAATG/TACAAA 1 -- us2k10--------
    rs1126976861,2
    --46769857(+) AAAGCA/GGTGAC 1 -- us2k11Minor allele frequency- G:0.00CSA 1
    rs1809595801,2
    --46770302(+) GTAAAC/TGAAAA 2 -- us2k10--------
    rs1854335871,2
    --46770766(+) AAGGTC/TTGTTG 2 -- us2k10--------
    rs59062891,2
    C,--46770843(+) ATATAC/TACACA 2 -- us2k11Minor allele frequency- T:0.00NA 2
    rs1997573501,2
    --46770863(+) TATAT-/ATAC  
            
    ATACA
    2 -- us2k10--------
    rs1390683211,2
    --46770960(+) AAGAAC/TGCGTG 2 -- us2k10--------
    rs1498812191,2
    --46771010(+) CTTCGA/GAGCTA 2 -- us2k10--------
    rs1909712901,2
    --46771179(+) CTGATA/TGAAAG 2 -- us2k10--------
    rs1448751671,2
    --46771399(+) ACTGAA/CTAAAT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for PHF16 (46771711 - 46920641 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 13 variations for PHF16
         4 CNVs: 96631 83485 73967 9342
         1 Indel: 96633
         8 Inversions: 37373 29456 37372 103383 37371 37374 29457 0658
    Locus Specific Mutation Databases (LSDB): PHF16

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    PHF16 for disorders           About GeneDecksing

    OMIM gene information: 300618    OMIM disorders: --

    1 disease for PHF16:    About MalaCards
    breast cancer


    Export disorders for PHF16 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)
    About This Section

    PubMed articles for PHF16 gene, integrated from 9 sources (see all 20):
    (articles sorted by number of sources associating them with PHF16)
        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. (2006)
    2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (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. (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. (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. (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. (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. (1996)
    9. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    10. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)

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

    (According to HUGE)
    About This Section
    HUGE: KIAA0215

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PHF16 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PHF16 gene:
    Search GeneIP for patents involving PHF16

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



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