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Protein

Histone lysine demethylase PHF8

Gene

PHF8

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 H3K4me3.10 Publications

Catalytic activityi

Protein N6,N(6)-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO2.
Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2.

Cofactori

Fe2+2 PublicationsNote: Binds 1 Fe2+ ion per subunit.2 Publications

Kineticsi

  1. KM=134 µM for histone H3 H3K9Me21 Publication
  2. KM=8 µM for histone H3 H3K4me3 and H3K9Me21 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei280Substrate1
    Metal bindingi283Iron; catalyticPROSITE-ProRule annotation2 Publications1
    Metal bindingi285Iron; catalyticPROSITE-ProRule annotation2 Publications1
    Binding sitei300Substrate1
    Metal bindingi355Iron; catalyticPROSITE-ProRule annotation2 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri41 – 92PHD-typePROSITE-ProRule annotationAdd BLAST52

    GO - Molecular functioni

    • chromatin binding Source: UniProtKB
    • histone demethylase activity Source: UniProtKB
    • histone demethylase activity (H3-K27 specific) Source: UniProtKB
    • histone demethylase activity (H3-K36 specific) Source: UniProtKB
    • histone demethylase activity (H3-K9 specific) Source: UniProtKB
    • histone demethylase activity (H4-K20 specific) Source: UniProtKB
    • iron ion binding Source: UniProtKB
    • methylated histone binding Source: UniProtKB
    • 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 Source: UniProtKB
    • zinc ion binding Source: UniProtKB

    GO - Biological processi

    • brain development Source: UniProtKB
    • G1/S transition of mitotic cell cycle Source: UniProtKB
    • histone H3-K27 demethylation Source: UniProtKB
    • histone H3-K36 demethylation Source: UniProtKB
    • histone H3-K9 demethylation Source: UniProtKB
    • histone H4-K20 demethylation Source: UniProtKB
    • negative regulation of chromatin silencing at rDNA Source: UniProtKB
    • positive regulation of transcription, DNA-templated Source: UniProtKB
    • positive regulation of transcription from RNA polymerase I promoter Source: UniProtKB
    • transcription, DNA-templated Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Activator, Chromatin regulator, Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Cell cycle, Transcription, Transcription regulation

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000172943-MONOMER.
    ReactomeiR-HSA-2299718. Condensation of Prophase Chromosomes.
    R-HSA-3214842. HDMs demethylate histones.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone lysine demethylase PHF8 (EC:1.14.11.27)
    Alternative name(s):
    PHD finger protein 8
    Gene namesi
    Name:PHF8
    Synonyms:KIAA1111, ZNF422
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome X

    Organism-specific databases

    HGNCiHGNC:20672. PHF8.

    Subcellular locationi

    • Nucleus
    • Nucleusnucleolus

    • Note: Recruited to H3K4me3 sites on chromatin during interphase. Dissociates from chromatin when cells enter mitosis.

    GO - Cellular componenti

    • nuclear membrane Source: HPA
    • nucleolus Source: UniProtKB
    • nucleoplasm Source: Reactome
    • nucleus Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Mental retardation, X-linked, syndromic, Siderius type (MRXSSD)2 Publications
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionA syndrome characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.
    See also OMIM:300263
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_062250315F → S in MRXSSD; abolishes histone methyltransferase activity. 8 PublicationsCorresponds to variant rs121918524dbSNPEnsembl.1

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi43Y → A: Abolishes binding to H3K4me3; when associated with A-50. 2 Publications1
    Mutagenesisi50Y → A: Abolishes binding to H3K4me3; when associated with A-43. Abolishes binding to H3K4me3; when associated with A-65. 1 Publication1
    Mutagenesisi65W → A: Abolishes binding to H3K4me3; when associated with A-50. 1 Publication1
    Mutagenesisi69S → A: Impairs phosphorylation by CDK1 and dissociation from chromatin when cells enter mitosis; when associated with A-120. 1 Publication1
    Mutagenesisi120S → A: Impairs phosphorylation by CDK1 and dissociation from chromatin when cells enter mitosis; when associated with A-69. 1 Publication1
    Mutagenesisi283 – 285HID → AAA: Abolishes histone methyltransferase activity. 1 Publication3
    Mutagenesisi283H → A: Abolishes histone methyltransferase activity. 3 Publications1

    Keywords - Diseasei

    Disease mutation, Mental retardation

    Organism-specific databases

    DisGeNETi23133.
    MalaCardsiPHF8.
    MIMi300263. phenotype.
    OpenTargetsiENSG00000172943.
    Orphaneti85287. X-linked intellectual disability, Siderius type.
    PharmGKBiPA134889361.

    Chemistry databases

    ChEMBLiCHEMBL1938212.
    GuidetoPHARMACOLOGYi2698.

    Polymorphism and mutation databases

    BioMutaiPHF8.
    DMDMi73620986.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000592951 – 1060Histone lysine demethylase PHF8Add BLAST1060

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei69Phosphoserine; by CDK11 Publication1
    Modified residuei120Phosphoserine; by CDK1Combined sources1 Publication1
    Modified residuei651PhosphoserineCombined sources1
    Modified residuei704PhosphotyrosineBy similarity1
    Modified residuei705PhosphothreonineCombined sources1
    Modified residuei706PhosphothreonineCombined sources1
    Modified residuei722PhosphoserineCombined sources1
    Modified residuei804PhosphoserineCombined sources1
    Modified residuei826PhosphoserineBy similarity1
    Modified residuei834PhosphoserineBy similarity1
    Modified residuei854PhosphoserineCombined sources1
    Modified residuei857PhosphoserineCombined sources1
    Modified residuei880PhosphoserineCombined sources1

    Post-translational modificationi

    Phosphorylation at Ser-69 and Ser-120 are required for dissociation from chromatin and accumulation of H4K20Me1 levels during prophase.1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    EPDiQ9UPP1.
    PaxDbiQ9UPP1.
    PeptideAtlasiQ9UPP1.
    PRIDEiQ9UPP1.

    PTM databases

    iPTMnetiQ9UPP1.
    PhosphoSitePlusiQ9UPP1.
    SwissPalmiQ9UPP1.

    Expressioni

    Gene expression databases

    BgeeiENSG00000172943.
    CleanExiHS_PHF8.
    ExpressionAtlasiQ9UPP1. baseline and differential.
    GenevisibleiQ9UPP1. HS.

    Organism-specific databases

    HPAiHPA038779.
    HPA062015.

    Interactioni

    Subunit structurei

    Interacts with POLR1B, UBTF, SETD1A, HCFC1, E2F1 and ZNF711.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PML-RARQ151566EBI-6601215,EBI-867256
    RARAP102762EBI-6601215,EBI-413374

    GO - Molecular functioni

    • methylated histone binding Source: UniProtKB

    Protein-protein interaction databases

    BioGridi116751. 56 interactors.
    DIPiDIP-38913N.
    IntActiQ9UPP1. 29 interactors.
    MINTiMINT-4651164.
    STRINGi9606.ENSP00000350676.

    Chemistry databases

    BindingDBiQ9UPP1.

    Structurei

    Secondary structure

    11060
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni44 – 47Combined sources4
    Beta strandi56 – 58Combined sources3
    Turni60 – 62Combined sources3
    Beta strandi65 – 67Combined sources3
    Helixi68 – 71Combined sources4
    Helixi75 – 78Combined sources4
    Beta strandi81 – 83Combined sources3
    Helixi87 – 93Combined sources7
    Helixi121 – 129Combined sources9
    Turni136 – 138Combined sources3
    Turni144 – 146Combined sources3
    Helixi149 – 155Combined sources7
    Beta strandi161 – 165Combined sources5
    Turni167 – 170Combined sources4
    Helixi180 – 187Combined sources8
    Beta strandi192 – 197Combined sources6
    Turni198 – 201Combined sources4
    Beta strandi202 – 207Combined sources6
    Helixi208 – 215Combined sources8
    Beta strandi224 – 230Combined sources7
    Helixi235 – 238Combined sources4
    Helixi244 – 249Combined sources6
    Helixi251 – 255Combined sources5
    Beta strandi270 – 274Combined sources5
    Beta strandi278 – 283Combined sources6
    Helixi286 – 288Combined sources3
    Beta strandi290 – 305Combined sources16
    Helixi309 – 319Combined sources11
    Helixi324 – 326Combined sources3
    Helixi329 – 331Combined sources3
    Beta strandi332 – 334Combined sources3
    Beta strandi337 – 342Combined sources6
    Beta strandi346 – 349Combined sources4
    Beta strandi354 – 370Combined sources17
    Beta strandi373 – 375Combined sources3
    Helixi376 – 389Combined sources14
    Helixi393 – 395Combined sources3
    Helixi400 – 420Combined sources21
    Helixi427 – 444Combined sources18
    Turni446 – 448Combined sources3
    Helixi449 – 451Combined sources3
    Helixi453 – 455Combined sources3
    Helixi462 – 477Combined sources16

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2WWUX-ray2.15A115-483[»]
    3K3NX-ray2.40A122-483[»]
    3K3OX-ray2.10A122-483[»]
    3KV4X-ray2.19A37-483[»]
    4DO0X-ray2.55A115-483[»]
    ProteinModelPortaliQ9UPP1.
    SMRiQ9UPP1.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9UPP1.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini231 – 387JmjCPROSITE-ProRule annotationAdd BLAST157

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni101 – 115LinkerAdd BLAST15

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi769 – 807Ser-richAdd BLAST39

    Domaini

    The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 promotes its access to H3K9me2.
    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.

    Sequence similaritiesi

    Contains 1 JmjC domain.PROSITE-ProRule annotation
    Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri41 – 92PHD-typePROSITE-ProRule annotationAdd BLAST52

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiKOG1633. Eukaryota.
    ENOG410XQXU. LUCA.
    GeneTreeiENSGT00550000074396.
    HOGENOMiHOG000231232.
    HOVERGENiHBG045631.
    InParanoidiQ9UPP1.
    KOiK19415.
    OMAiLGTCFKD.
    OrthoDBiEOG091G09DB.
    PhylomeDBiQ9UPP1.
    TreeFamiTF106480.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003347. JmjC_dom.
    IPR019786. Zinc_finger_PHD-type_CS.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF02373. JmjC. 1 hit.
    PF00628. PHD. 1 hit.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51184. JMJC. 1 hit.
    PS01359. ZF_PHD_1. 1 hit.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]

    Sequences (5)i

    Sequence statusi: Complete.

    This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q9UPP1-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MNRSRAIVQR GRVLPPPAPL DTTNLAGRRT LQGRAKMASV PVYCLCRLPY
    60 70 80 90 100
    DVTRFMIECD MCQDWFHGSC VGVEEEKAAD IDLYHCPNCE VLHGPSIMKK
    110 120 130 140 150
    RRGSSKGHDT HKGKPVKTGS PTFVRELRSR TFDSSDEVIL KPTGNQLTVE
    160 170 180 190 200
    FLEENSFSVP ILVLKKDGLG MTLPSPSFTV RDVEHYVGSD KEIDVIDVTR
    210 220 230 240 250
    QADCKMKLGD FVKYYYSGKR EKVLNVISLE FSDTRLSNLV ETPKIVRKLS
    260 270 280 290 300
    WVENLWPEEC VFERPNVQKY CLMSVRDSYT DFHIDFGGTS VWYHVLKGEK
    310 320 330 340 350
    IFYLIRPTNA NLTLFECWSS SSNQNEMFFG DQVDKCYKCS VKQGQTLFIP
    360 370 380 390 400
    TGWIHAVLTP VDCLAFGGNF LHSLNIEMQL KAYEIEKRLS TADLFRFPNF
    410 420 430 440 450
    ETICWYVGKH ILDIFRGLRE NRRHPASYLV HGGKALNLAF RAWTRKEALP
    460 470 480 490 500
    DHEDEIPETV RTVQLIKDLA REIRLVEDIF QQNVGKTSNI FGLQRIFPAG
    510 520 530 540 550
    SIPLTRPAHS TSVSMSRLSL PSKNGSKKKG LKPKELFKKA ERKGKESSAL
    560 570 580 590 600
    GPAGQLSYNL MDTYSHQALK TGSFQKAKFN ITGACLNDSD DDSPDLDLDG
    610 620 630 640 650
    NESPLALLMS NGSTKRVKSL SKSRRTKIAK KVDKARLMAE QVMEDEFDLD
    660 670 680 690 700
    SDDELQIDER LGKEKATLII RPKFPRKLPR AKPCSDPNRV REPGEVEFDI
    710 720 730 740 750
    EEDYTTDEDM VEGVEGKLGN GSGAGGILDL LKASRQVGGP DYAALTEAPA
    760 770 780 790 800
    SPSTQEAIQG MLCMANLQSS SSSPATSSLQ AWWTGGQDRS SGSSSSGLGT
    810 820 830 840 850
    VSNSPASQRT PGKRPIKRPA YWRTESEEEE ENASLDEQDS LGACFKDAEY
    860 870 880 890 900
    IYPSLESDDD DPALKSRPKK KKNSDDAPWS PKARVTPTLP KQDRPVREGT
    910 920 930 940 950
    RVASIETGLA AAAAKLAQQE LQKAQKKKYI KKKPLLKEVE QPRPQDSNLS
    960 970 980 990 1000
    LTVPAPTVAA TPQLVTSSSP LPPPEPKQEA LSGSLADHEY TARPNAFGMA
    1010 1020 1030 1040 1050
    QANRSTTPMA PGVFLTQRRP SVGSQSNQAG QGKRPKKGLA TAKQRLGRIL
    1060
    KIHRNGKLLL
    Length:1,060
    Mass (Da):117,864
    Last modified:August 16, 2005 - v3
    Checksum:i04C83D7C5E9E56B8
    GO
    Isoform 2 (identifier: Q9UPP1-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-36: Missing.

    Show »
    Length:1,024
    Mass (Da):113,913
    Checksum:i75773C0918578FB0
    GO
    Isoform 3 (identifier: Q9UPP1-3) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         478-578: Missing.

    Note: No experimental confirmation available.
    Show »
    Length:959
    Mass (Da):106,902
    Checksum:iF54BE8A814BF1701
    GO
    Isoform 4 (identifier: Q9UPP1-4) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-36: Missing.
         478-578: Missing.
         1060-1060: L → LRQVIVQAECRQAIHEPKLKRRDAHP

    Note: No experimental confirmation available.
    Show »
    Length:948
    Mass (Da):105,913
    Checksum:iF32740CB7A2CE3F6
    GO
    Isoform 5 (identifier: Q9UPP1-5) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-36: Missing.
         717-746: KLGNGSGAGGILDLLKASRQVGGPDYAALT → YQTATPAPAQGAS
         920-931: ELQKAQKKKYIK → VKKMKLSLTDSG
         932-1060: Missing.

    Show »
    Length:878
    Mass (Da):98,290
    Checksum:i690CE764C0C28D28
    GO

    Sequence cautioni

    The sequence BAA83063 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence BAB13877 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
    The sequence CAI45929 differs from that shown. Reason: Erroneous termination at position 419. Translated as Arg.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti232S → P in BAB13877 (PubMed:12168954).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_062250315F → S in MRXSSD; abolishes histone methyltransferase activity. 8 PublicationsCorresponds to variant rs121918524dbSNPEnsembl.1
    Natural variantiVAR_076254969Missing Found in patients with autism spectrum disorders; unknown pathological significance. 1 Publication1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0149641 – 36Missing in isoform 2, isoform 4 and isoform 5. 3 PublicationsAdd BLAST36
    Alternative sequenceiVSP_014965478 – 578Missing in isoform 3 and isoform 4. 1 PublicationAdd BLAST101
    Alternative sequenceiVSP_054019717 – 746KLGNG…YAALT → YQTATPAPAQGAS in isoform 5. 1 PublicationAdd BLAST30
    Alternative sequenceiVSP_054020920 – 931ELQKA…KKYIK → VKKMKLSLTDSG in isoform 5. 1 PublicationAdd BLAST12
    Alternative sequenceiVSP_054021932 – 1060Missing in isoform 5. 1 PublicationAdd BLAST129
    Alternative sequenceiVSP_0436401060L → LRQVIVQAECRQAIHEPKLK RRDAHP in isoform 4. 1 Publication1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB029034 mRNA. Translation: BAA83063.1. Different initiation.
    CR933612 mRNA. Translation: CAI45929.1. Sequence problems.
    AK021696 mRNA. Translation: BAB13877.1. Different initiation.
    AK022788 mRNA. Translation: BAG51116.1.
    AK304272 mRNA. Translation: BAH14147.1.
    AL589872 Genomic DNA. No translation available.
    AL732374 Genomic DNA. No translation available.
    Z98051 Genomic DNA. No translation available.
    BC042108 mRNA. No translation available.
    BC053861 mRNA. Translation: AAH53861.1.
    CCDSiCCDS14355.1. [Q9UPP1-2]
    CCDS55418.1. [Q9UPP1-4]
    CCDS55419.1. [Q9UPP1-5]
    CCDS55420.1. [Q9UPP1-1]
    RefSeqiNP_001171825.1. NM_001184896.1. [Q9UPP1-1]
    NP_001171826.1. NM_001184897.1. [Q9UPP1-4]
    NP_055922.1. NM_015107.2. [Q9UPP1-2]
    XP_016884851.1. XM_017029362.1. [Q9UPP1-2]
    UniGeneiHs.133352.

    Genome annotation databases

    EnsembliENST00000322659; ENSP00000319473; ENSG00000172943. [Q9UPP1-5]
    ENST00000338154; ENSP00000338868; ENSG00000172943. [Q9UPP1-2]
    ENST00000338946; ENSP00000340051; ENSG00000172943. [Q9UPP1-4]
    ENST00000357988; ENSP00000350676; ENSG00000172943. [Q9UPP1-1]
    GeneIDi23133.
    KEGGihsa:23133.
    UCSCiuc004dst.4. human. [Q9UPP1-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB029034 mRNA. Translation: BAA83063.1. Different initiation.
    CR933612 mRNA. Translation: CAI45929.1. Sequence problems.
    AK021696 mRNA. Translation: BAB13877.1. Different initiation.
    AK022788 mRNA. Translation: BAG51116.1.
    AK304272 mRNA. Translation: BAH14147.1.
    AL589872 Genomic DNA. No translation available.
    AL732374 Genomic DNA. No translation available.
    Z98051 Genomic DNA. No translation available.
    BC042108 mRNA. No translation available.
    BC053861 mRNA. Translation: AAH53861.1.
    CCDSiCCDS14355.1. [Q9UPP1-2]
    CCDS55418.1. [Q9UPP1-4]
    CCDS55419.1. [Q9UPP1-5]
    CCDS55420.1. [Q9UPP1-1]
    RefSeqiNP_001171825.1. NM_001184896.1. [Q9UPP1-1]
    NP_001171826.1. NM_001184897.1. [Q9UPP1-4]
    NP_055922.1. NM_015107.2. [Q9UPP1-2]
    XP_016884851.1. XM_017029362.1. [Q9UPP1-2]
    UniGeneiHs.133352.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2WWUX-ray2.15A115-483[»]
    3K3NX-ray2.40A122-483[»]
    3K3OX-ray2.10A122-483[»]
    3KV4X-ray2.19A37-483[»]
    4DO0X-ray2.55A115-483[»]
    ProteinModelPortaliQ9UPP1.
    SMRiQ9UPP1.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi116751. 56 interactors.
    DIPiDIP-38913N.
    IntActiQ9UPP1. 29 interactors.
    MINTiMINT-4651164.
    STRINGi9606.ENSP00000350676.

    Chemistry databases

    BindingDBiQ9UPP1.
    ChEMBLiCHEMBL1938212.
    GuidetoPHARMACOLOGYi2698.

    PTM databases

    iPTMnetiQ9UPP1.
    PhosphoSitePlusiQ9UPP1.
    SwissPalmiQ9UPP1.

    Polymorphism and mutation databases

    BioMutaiPHF8.
    DMDMi73620986.

    Proteomic databases

    EPDiQ9UPP1.
    PaxDbiQ9UPP1.
    PeptideAtlasiQ9UPP1.
    PRIDEiQ9UPP1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000322659; ENSP00000319473; ENSG00000172943. [Q9UPP1-5]
    ENST00000338154; ENSP00000338868; ENSG00000172943. [Q9UPP1-2]
    ENST00000338946; ENSP00000340051; ENSG00000172943. [Q9UPP1-4]
    ENST00000357988; ENSP00000350676; ENSG00000172943. [Q9UPP1-1]
    GeneIDi23133.
    KEGGihsa:23133.
    UCSCiuc004dst.4. human. [Q9UPP1-1]

    Organism-specific databases

    CTDi23133.
    DisGeNETi23133.
    GeneCardsiPHF8.
    HGNCiHGNC:20672. PHF8.
    HPAiHPA038779.
    HPA062015.
    MalaCardsiPHF8.
    MIMi300263. phenotype.
    300560. gene.
    neXtProtiNX_Q9UPP1.
    OpenTargetsiENSG00000172943.
    Orphaneti85287. X-linked intellectual disability, Siderius type.
    PharmGKBiPA134889361.
    HUGEiSearch...
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG1633. Eukaryota.
    ENOG410XQXU. LUCA.
    GeneTreeiENSGT00550000074396.
    HOGENOMiHOG000231232.
    HOVERGENiHBG045631.
    InParanoidiQ9UPP1.
    KOiK19415.
    OMAiLGTCFKD.
    OrthoDBiEOG091G09DB.
    PhylomeDBiQ9UPP1.
    TreeFamiTF106480.

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000172943-MONOMER.
    ReactomeiR-HSA-2299718. Condensation of Prophase Chromosomes.
    R-HSA-3214842. HDMs demethylate histones.

    Miscellaneous databases

    ChiTaRSiPHF8. human.
    EvolutionaryTraceiQ9UPP1.
    GeneWikiiPHF8.
    GenomeRNAii23133.
    PROiQ9UPP1.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000172943.
    CleanExiHS_PHF8.
    ExpressionAtlasiQ9UPP1. baseline and differential.
    GenevisibleiQ9UPP1. HS.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003347. JmjC_dom.
    IPR019786. Zinc_finger_PHD-type_CS.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF02373. JmjC. 1 hit.
    PF00628. PHD. 1 hit.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51184. JMJC. 1 hit.
    PS01359. ZF_PHD_1. 1 hit.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPHF8_HUMAN
    AccessioniPrimary (citable) accession number: Q9UPP1
    Secondary accession number(s): B3KMV4
    , B7Z911, Q5H9U5, Q5JPR9, Q5JPS0, Q5JPS2, Q5JPS3, Q5VUJ4, Q7Z6D4, Q9HAH2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 19, 2004
    Last sequence update: August 16, 2005
    Last modified: November 2, 2016
    This is version 142 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome X
      Human chromosome X: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.