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PHF8 Gene

protein-coding   GIFtS: 64
GCID: GC0XM053979

PHD Finger Protein 8

  See PHF8-related disease
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
PHD Finger Protein 81 2 3     MRXSSD2 5
ZNF4222 3 5     KIAA11113 5
Jumonji C Domain-Containing Histone Demethylase 1F1 2     JHDM1F2
EC 1.14.11.273 8     Histone Lysine Demethylase PHF82

External Ids:    HGNC: 206721   Entrez Gene: 231332   Ensembl: ENSG000001729437   OMIM: 3005605   UniProtKB: Q9UPP13   

Export aliases for PHF8 gene to outside databases

Previous GC identifers: GC0XM052930 GC0XM053846 GC0XM051017


(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 PHF8 Gene:
The protein encoded by this gene is a histone lysine demethylase that preferentially acts on histones in the
monomethyl or dimethyl states. The encoded protein requires Fe(2+) ion, 2-oxoglutarate, and oxygen for its
catalytic activity. Defects in this gene are a cause of mental retardation syndromic X-linked Siderius type
(MRXSSD). Four transcript variants encoding different isoforms have been found for this gene. (provided by
RefSeq, May 2010)

GeneCards Summary for PHF8 Gene:
PHF8 (PHD finger protein 8) is a protein-coding gene. Diseases associated with PHF8 include x-linked intellectual disability, siderius type. GO annotations related to this gene include chromatin binding and methylated histone residue binding. An important paralog of this gene is PHF2.

UniProtKB/Swiss-Prot: PHF8_HUMAN, Q9UPP1
Function: Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell
cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3
'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20'
residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic
repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a
coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes.
Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity
toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May
also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains
unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase
specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2
when binding H3K4me3

Gene Wiki entry for PHF8 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 at NCBI GenBank:
NC_000023.10  NT_011630.15  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PHF8 gene promoter:
         Max1   E2F-3a   E2F-4   E2F-5   Pbx1a   E2F-2   C/EBPalpha   E2F   E2F-1   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPHF8 promoter sequence
   Search Chromatin IP Primers for PHF8

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PHF8


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

Entrez Gene cytogenetic band: Xp11.22   Ensembl cytogenetic band:  Xp11.22   HGNC cytogenetic band: Xp11.22

PHF8 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHF8 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM053979:  view genomic region     (about GC identifiers)

Start:
53,963,109 bp from pter      End:
54,075,391 bp from pter
Size:
112,283 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: PHF8_HUMAN, Q9UPP1 (See protein sequence)
Recommended Name: Histone lysine demethylase PHF8  
Size: 1060 amino acids; 117864 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (Probable)
Subunit: Interacts with POLR1B, UBTF, SETD1A, HCFC1, E2F1 and ZNF711
Sequence caution: Sequence=BAA83063.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=BAB13877.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAI41577.1;
Type=Erroneous gene model prediction; Sequence=CAI41581.1; Type=Erroneous gene model prediction;
Sequence=CAI41582.1; Type=Erroneous gene model prediction; Sequence=CAI42861.1; Type=Erroneous gene model
prediction; Sequence=CAI45929.1; Type=Erroneous termination; Positions=419; Note=Translated as Arg;
5 PDB 3D structures from and Proteopedia for PHF8:
2WWU (3D)        3K3N (3D)        3K3O (3D)        3KV4 (3D)        4DO0 (3D)    
Secondary accessions: B7Z911 Q5H9U5 Q5JPR9 Q5JPS0 Q5JPS2 Q5JPS3 Q5VUJ4 Q7Z6D4 Q9HAH2
Alternative splicing: 4 isoforms:  Q9UPP1-1   Q9UPP1-2   Q9UPP1-3   Q9UPP1-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PHF8: NX_Q9UPP1

Explore proteomics data for PHF8 at MOPED

Post-translational modifications: 

  • Phosphorylation at Ser-69 and Ser-120 are required for dissociation from chromatin and accumulation of H4K20Me1
    levels during prophase1
  • Ubiquitination2 at Lys467, Lys486, Lys732
  • Modification sites at PhosphoSitePlus
  • 2 DME Specific Peptides for PHF8 (Q9UPP1)
     GTSVWYH  TDFHIDF 


    See PHF8 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001171825.1  NP_001171826.1  NP_001171827.1  NP_055922.1  

    ENSEMBL proteins: 
     ENSP00000338868   ENSP00000350676   ENSP00000379578   ENSP00000397129   ENSP00000319473  
     ENSP00000388796   ENSP00000414028   ENSP00000408113   ENSP00000398995   ENSP00000404117  
     ENSP00000405897   ENSP00000410100   ENSP00000416546   ENSP00000340051  
    Reactome Protein details: Q9UPP1

    PHF8 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for PHF8

     
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    Cloud-Clone Corp. ELISAs for PHF8
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    Search eBioscience for ELISAs for PHF8 


    (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 6):
     IPR001965 Znf_PHD
     IPR013083 Znf_RING/FYVE/PHD
     IPR003347 JmjC_dom
     IPR019786 Zinc_finger_PHD-type_CS
     IPR011011 Znf_FYVE_PHD

    Graphical View of Domain Structure for InterPro Entry Q9UPP1

    ProtoNet protein and cluster: Q9UPP1

    UniProtKB/Swiss-Prot: PHF8_HUMAN, Q9UPP1
    Domain: The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 promotes its access to
    H3K9me2
    Domain: The linker region is a critical determinant of demethylase specificity. It enables the active site of JmjC
    to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3
    Similarity: Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily
    Similarity: Contains 1 JmjC domain
    Similarity: Contains 1 PHD-type zinc finger


    Find genes that share domains with PHF8           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PHF8_HUMAN, Q9UPP1
    Function: Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell
    cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3
    'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20'
    residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic
    repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a
    coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes.
    Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity
    toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May
    also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains
    unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase
    specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2
    when binding H3K4me3
    Catalytic activity: Protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine +
    succinate + formaldehyde + CO(2)
    Catalytic activity: Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate +
    formaldehyde + CO(2)
    Biophysicochemical properties: Kinetic parameters: KM=134 uM for histone H3 H3K9Me2; KM=8 uM for histone H3
    H3K4me3 and H3K9Me2;

         Enzyme Number (IUBMB): EC 1.14.11.271 2

         Gene Ontology (GO): Selected molecular function terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IDA--
    GO:0005506iron ion binding IDA--
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IDA--
    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 IDA--
         
    Find genes that share ontologies with PHF8           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for PHF8:
     Increased cell death in HCC-19  Small cells 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PHF8
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PHF8
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PHF8

    miRNA
    Products:
        
    miRTarBase miRNAs that target PHF8:
    hsa-mir-335-5p (MIRT019133), hsa-mir-1229-3p (MIRT036321), hsa-mir-20a-5p (MIRT050476), hsa-mir-193b-3p (MIRT041284), hsa-mir-744-5p (MIRT037650)

    Block miRNA regulation of human, mouse, rat PHF8 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PHF8 (see all 73):
    hsa-miR-323-3p hsa-miR-3130-5p hsa-miR-1321 hsa-miR-3938 hsa-miR-134 hsa-miR-3921 hsa-miR-629 hsa-miR-3148
    SwitchGear 3'UTR luciferase reporter plasmidPHF8 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PHF8

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    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHF8


    (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
    PHF8_HUMAN, Q9UPP1: Nucleus. Nucleus, nucleolus. Note=Recruited to H3K4me3 sites on chromatin during interphase.
    Dissociates from chromatin when cells enter mitosis
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    cytoskeleton1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005730nucleolus IDA--
    GO:0015630microtubule cytoskeleton IDA--

    Find genes that share ontologies with PHF8           About GenesLikeMe


    (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 PHF8 About    
    See pathways by source

    SuperPathContained pathways About
    1Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    M Phase0.62
    Cell Cycle0.90
    2RNA Polymerase I Promoter Opening
    Condensation of Prophase Chromosomes0.78
    Mitotic Prophase0.56


    Find genes that share SuperPaths with PHF8           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for PHF8
        Condensation of Prophase Chromosomes


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PHF8
    Interactions:

        Search GeneGlobe Interaction Network for PHF8

    STRING Interaction Network Preview (showing 5 interactants - click image to see 21)

    Selected Interacting proteins for PHF8 (Q9UPP11, 2, 3 ENSP000003388684) via UniProtKB, MINT, STRING, and/or I2D (see all 34)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H3AP684313, ENSP000003502754I2D: score=1 STRING: ENSP00000350275
    HIST1H3BP684313I2D: score=1 
    HIST1H3CP684313I2D: score=1 
    HIST1H3DP684313I2D: score=1 
    HIST1H3EP684313I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000082G1/S transition of mitotic cell cycle IMP--
    GO:0000278mitotic cell cycle TAS--
    GO:0006351transcription, DNA-templated IEA--
    GO:0007420brain development ISS--
    GO:0033169histone H3-K9 demethylation IDA--

    Find genes that share ontologies with PHF8           About GenesLikeMe



    (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 PHF8



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PHF8 gene (4 alternative transcripts): 
    NM_001184896.1  NM_001184897.1  NM_001184898.1  NM_015107.2  

    Unigene Cluster for PHF8:

    PHD finger protein 8
    Hs.133352  [show with all ESTs]
    Unigene Representative Sequence: NM_015107
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000338154(uc004dst.3 uc004dsw.3) ENST00000357988(uc004dsv.3 uc004dsu.3)
    ENST00000396282 ENST00000470103 ENST00000443302(uc004dsx.3) ENST00000322659(uc004dsy.3)
    ENST00000494928 ENST00000413386 ENST00000448003 ENST00000490635 ENST00000425862
    ENST00000437224 ENST00000415025 ENST00000453905 ENST00000433120 ENST00000445025
    ENST00000462182 ENST00000338946
    miRNA
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    hsa-miR-323-3p hsa-miR-3130-5p hsa-miR-1321 hsa-miR-3938 hsa-miR-134 hsa-miR-3921 hsa-miR-629 hsa-miR-3148
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      QuantiFast Probe-based Assays in human, mouse, rat PHF8

    Additional mRNA sequence: 

    AB029034.1 AF091081.1 AK021696.1 AK022788.1 AK027229.1 AK304272.1 BC017720.1 BC042108.1 
    BC053861.1 

    11 DOTS entries:

    DT.438059  DT.95190888  DT.100673818  DT.315809  DT.403513  DT.100779272  DT.121277602  DT.40268452 
    DT.40124634  DT.426008  DT.92431243 

    Selected AceView cDNA sequences (see all 190):

    BU173122 CR626598 BQ943912 AB029034 BU195738 BG957307 AL704568 CA438369 
    CR595374 BX091300 BG034552 BG939390 AK021696 BC042108 AL157527 AI758427 
    CA314327 AA358691 CB117346 AU125416 AA358692 AW953631 AA908193 CD244226 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PHF8 (see all 12)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ·
    SP1:        -     -     -     -                                                                                         -                 -                     
    SP2:                          -                                                                                         -                 -                     
    SP3:                                                                                                                    -                 -                     
    SP4:                                                                                                                    -           -     -                     
    SP5:                                                                                                                    -                 -                     

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


    ECgene alternative splicing isoforms for PHF8

    (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)
    About This Section

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    PHF8 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PHF8 Expression
    About this image

    PHF8 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PHF8 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.133352
        Custom PCR Arrays for PHF8
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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 PHF8 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Phf81 , 5 PHD finger protein 81, 5 90.84(n)1
    94.62(a)1
      X (68.46 cM)5
    3205951  NM_001113354.11  NP_001106825.11 
     1515206725 
    lizard
    (Anolis carolinensis)
    Reptilia PHF86
    PHD finger protein 8
    72(a)
    1 ↔ 1
    1(205559669-205596572)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3986832 hypothetical protein LOC398683 76.41(n)    BC056031.1 
    zebrafish
    (Danio rerio)
    Actinopterygii phf81 PHD finger protein 8 64.65(n)
    67.52(a)
      566534  NM_001202447.1  NP_001189376.1 
    worm
    (Caenorhabditis elegans)
    Secernentea jmjd-1.16
    jmjd-1.26
    Protein JMJD-1.1 (jmjd-1.1) mRNA, complete cds
    Protein JMJD-1.2, isoform a (jmjd-1.2) mRNA, compl...
    27(a)
    20(a)
    many ↔ many
    many ↔ many
    II(11806567-11808829) WBGene00005013
    IV(4660991-4665208) WBGene00017920
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes JHD16
    JmjC domain family histone demethylase specific fo...
    29(a)
    1 → many
    V(254656-256134) YER051W


    ENSEMBL Gene Tree for PHF8 (if available)
    TreeFam Gene Tree for PHF8 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PHF8 gene
    PHF22  KDM2A2  KDM7A2  KDM2B2  FBXL192  
    12 SIMAP similar genes for PHF8 using alignment to 10 protein entries:     PHF8_HUMAN (see all proteins):
    KDM7A    KDM2B    KDM2A    KDM5D    BPTF    FBXL10
    PHF2    JHDM1D    DIDO1    CXXC1    UBR7    PHF3

    Find genes that share paralogs with PHF8           About GenesLikeMe



    (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 PHF8 (see all 1274)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0622504
    Mental retardation, X-linked, syndromic, Siderius type (MRXSSD)4--see VAR_0622502 F S mis40--------
    rs1134022141,2
    C,F--53976890(+) AGTGCA/GATAAT 3 -- ds50011Minor allele frequency- G:0.00CSA 1
    rs2019474051,2
    --53977002(+) GAAAG-/AAAAAA 3 -- ds50010--------
    rs1998788851,2
    --53977306(+) ATCAC-/AAAAAA 3 -- ds50010--------
    rs1809788901,2
    --53977425(+) AGACAA/GGGACA 3 -- ut310--------
    rs1853051711,2
    --53977599(+) GGTGAA/GTAGAA 3 -- ut310--------
    rs78927821,2
    C,F,A,H--53977845(+) GGCTCT/CAAGAA 3 -- ut31 ese316Minor allele frequency- C:0.16NS EA NA 1789
    rs1896835121,2
    --53978443(+) AGTGGA/GTGGTA 3 -- ut310--------
    rs1813773081,2
    --53978529(+) AGATTG/TCCAGT 3 -- ut310--------
    rs2009730891,2
    --53978624(+) TGGAT-/GGTCTG 3 -- ut310--------

    HapMap Linkage Disequilibrium report for PHF8 (53963109 - 54075391 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for PHF8:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2740175CNV Deletion23290073
    nsv435891CNV Deletion17901297
    esv2675498CNV Deletion23128226
    nsv524220CNV Gain19592680

    Human Gene Mutation Database (HGMD): PHF8
    Locus Specific Mutation Databases (LSDB): PHF8

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PHF8
    DNA2.0 Custom Variant and Variant Library Synthesis for PHF8

    (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.)
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    OMIM gene information: 300560   
    OMIM disorders: 300263  
    UniProtKB/Swiss-Prot: PHF8_HUMAN, Q9UPP1
  • Mental retardation, X-linked, syndromic, Siderius type (MRXSSD) [MIM:300263]: A syndrome characterized by
    mild to borderline mental retardation with or without cleft lip/cleft palate. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 1 disease for PHF8:    
    About MalaCards
    x-linked intellectual disability, siderius type

    3 diseases from the University of Copenhagen DISEASES database for PHF8:
    Cleft lip     Intellectual disability     Cleft palate

    Find genes that share disorders with PHF8           About GenesLikeMe

    Genetic Association Database (GAD): PHF8
    Human Genome Epidemiology (HuGE) Navigator: PHF8 (1 document)

    Export disorders for PHF8 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 PHF8 gene, integrated from 10 sources (see all 50):
    (articles sorted by number of sources associating them with PHF8)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. (PubMed id 20023638)1, 2, 3 Horton J.R.... Cheng X. (Nat. Struct. Mol. Biol. 2010)
    2. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10470851)1, 2, 3 Kikuno R.... Ohara O. (DNA Res. 1999)
    3. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. (PubMed id 20208542)1, 2, 9 Feng W.... Grummt I. (Nat. Struct. Mol. Biol. 2010)
    4. Crystal structure of the PHF8 Jumonji domain, an N(epsilon)-methyl lysine demethylase. (PubMed id 20067792)1, 2, 9 Yue W.W.... McDonough M.A. (FEBS Lett. 2010)
    5. Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate. (PubMed id 17661819)1, 2, 9 Koivisto A.M....Jaervelae I. (Clin. Genet. 2007)
    6. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. (PubMed id 16199551)1, 2, 9 Laumonnier F.... Briault S. (J. Med. Genet. 2005)
    7. Case-case genome-wide association analysis shows markers differentially associated with schizophrenia and bipolar disorder and implicates calcium channel genes. (PubMed id 21057379)1, 4 Curtis D....Gurling H.M. (Psychiatr. Genet. 2011)
    8. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. (PubMed id 20346720)1, 2 Kleine-Kohlbrecher D....Helin K. (Mol. Cell 2010)
    9. The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. (PubMed id 20548336)1, 2 Qiu J.... Wong J. (Cell Res. 2010)
    10. PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. (PubMed id 20622854)1, 2 Liu W.... Rosenfeld M.G. (Nature 2010)

    (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: 23133 HGNC: 20672 AceView: PHF8 Ensembl:ENSG00000172943 euGenes: HUgn23133
    ECgene: PHF8 H-InvDB: PHF8

    (According to HUGE)
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    HUGE: KIAA1111

    (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 PHF8 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 PHF8 gene:
    Search GeneIP for patents involving PHF8

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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