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Q86YI8

- PHF13_HUMAN

UniProt

Q86YI8 - PHF13_HUMAN

Protein

PHD finger protein 13

Gene

PHF13

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 96 (01 Oct 2014)
      Sequence version 2 (05 May 2009)
      Previous versions | rss
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    Functioni

    Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri232 – 28049PHD-typeAdd
    BLAST

    GO - Molecular functioni

    1. chromatin binding Source: UniProtKB
    2. methylated histone binding Source: UniProtKB
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. chromatin modification Source: UniProtKB-KW
    2. chromosome segregation Source: UniProtKB
    3. mitotic cell cycle Source: UniProtKB
    4. mitotic chromosome condensation Source: UniProtKB

    Keywords - Molecular functioni

    Chromatin regulator

    Keywords - Biological processi

    Cell cycle, Cell division, DNA condensation, Mitosis

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    PHD finger protein 13
    Alternative name(s):
    Survival time-associated PHD finger protein in ovarian cancer 1
    Short name:
    SPOC1
    Gene namesi
    Name:PHF13
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:22983. PHF13.

    Subcellular locationi

    Nucleus 1 Publication. Nucleusnucleoplasm 1 Publication
    Note: Predominantly bound to chromatin, but a minor proportion is also detected in the nucleoplasm.

    GO - Cellular componenti

    1. nucleoplasm Source: UniProtKB-SubCell
    2. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134901883.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 300300PHD finger protein 13PRO_0000059304Add
    BLAST

    Post-translational modificationi

    Subject to proteasomal degradation. Stable when bound to chromatin. The soluble form is rapidly degraded.

    Proteomic databases

    PaxDbiQ86YI8.
    PRIDEiQ86YI8.

    PTM databases

    PhosphoSiteiQ86YI8.

    Expressioni

    Inductioni

    Expression levels are tightly regulated during the cell cycle. Strongly up-regulated during late G2 phase and M phase of the mitotic cell cycle. Down-regulated at the G1-S phase transition of the cell cycle.1 Publication

    Gene expression databases

    BgeeiQ86YI8.
    CleanExiHS_PHF13.
    GenevestigatoriQ86YI8.

    Organism-specific databases

    HPAiHPA026830.

    Interactioni

    Subunit structurei

    Interacts with histone H3 that is trimethylated at 'Lys-4' (H3K4me3). Interacts with GSK3B.2 Publications

    Protein-protein interaction databases

    BioGridi127151. 1 interaction.
    IntActiQ86YI8. 1 interaction.
    STRINGi9606.ENSP00000366876.

    Structurei

    Secondary structure

    1
    300
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi246 – 2483
    Turni250 – 2523
    Beta strandi255 – 2573
    Turni258 – 2625
    Helixi265 – 2673
    Helixi275 – 2784

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3O70X-ray1.85A232-281[»]
    3O7AX-ray1.67A229-280[»]
    ProteinModelPortaliQ86YI8.
    SMRiQ86YI8. Positions 229-280.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ86YI8.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni241 – 2488Interaction with trimethylated histone H3 (H3K4)

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi110 – 12718Nuclear localization signalCuratedAdd
    BLAST

    Sequence similaritiesi

    Contains 1 PHD-type zinc finger.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri232 – 28049PHD-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG281703.
    HOGENOMiHOG000010286.
    HOVERGENiHBG071437.
    InParanoidiQ86YI8.
    OMAiCFGHLQP.
    OrthoDBiEOG7ZKSCH.
    PhylomeDBiQ86YI8.
    TreeFamiTF331373.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF00628. PHD. 1 hit.
    [Graphical view]
    SMARTiSM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q86YI8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDSDSCAAAF HPEEYSPSCK RRRTVEDFNK FCTFVLAYAG YIPYPKEELP    50
    LRSSPSPANS TAGTIDSDGW DAGFSDIASS VPLPVSDRCF SHLQPTLLQR 100
    AKPSNFLLDR KKTDKLKKKK KRKRRDSDAP GKEGYRGGLL KLEAADPYVE 150
    TPTSPTLQDI PQAPSDPCSG WDSDTPSSGS CATVSPDQVK EIKTEGKRTI 200
    VRQGKQVVFR DEDSTGNDED IMVDSDDDSW DLVTCFCMKP FAGRPMIECN 250
    ECHTWIHLSC AKIRKSNVPE VFVCQKCRDS KFDIRRSNRS RTGSRKLFLD 300
    Length:300
    Mass (Da):33,582
    Last modified:May 5, 2009 - v2
    Checksum:i197663A113B995F2
    GO

    Sequence cautioni

    The sequence AAH32792.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.
    The sequence BAD92781.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti111 – 1111K → R in BAG53519. (PubMed:14702039)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti20 – 201K → E.1 Publication
    Corresponds to variant rs17853850 [ dbSNP | Ensembl ].
    VAR_055285

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK315110 mRNA. Translation: BAG37568.1.
    AK097715 mRNA. Translation: BAG53519.1.
    AB209544 mRNA. Translation: BAD92781.1. Different initiation.
    AL031447 Genomic DNA. Translation: CAI19471.1.
    CH471130 Genomic DNA. Translation: EAW71561.1.
    BC032792 mRNA. Translation: AAH32792.2. Different initiation.
    BC038516 mRNA. Translation: AAH38516.1.
    AL121733 mRNA. Translation: CAB57324.1.
    CCDSiCCDS85.1.
    RefSeqiNP_722519.2. NM_153812.2.
    UniGeneiHs.516079.

    Genome annotation databases

    EnsembliENST00000377648; ENSP00000366876; ENSG00000116273.
    GeneIDi148479.
    KEGGihsa:148479.
    UCSCiuc001aob.4. human.

    Polymorphism databases

    DMDMi229462750.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK315110 mRNA. Translation: BAG37568.1 .
    AK097715 mRNA. Translation: BAG53519.1 .
    AB209544 mRNA. Translation: BAD92781.1 . Different initiation.
    AL031447 Genomic DNA. Translation: CAI19471.1 .
    CH471130 Genomic DNA. Translation: EAW71561.1 .
    BC032792 mRNA. Translation: AAH32792.2 . Different initiation.
    BC038516 mRNA. Translation: AAH38516.1 .
    AL121733 mRNA. Translation: CAB57324.1 .
    CCDSi CCDS85.1.
    RefSeqi NP_722519.2. NM_153812.2.
    UniGenei Hs.516079.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3O70 X-ray 1.85 A 232-281 [» ]
    3O7A X-ray 1.67 A 229-280 [» ]
    ProteinModelPortali Q86YI8.
    SMRi Q86YI8. Positions 229-280.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 127151. 1 interaction.
    IntActi Q86YI8. 1 interaction.
    STRINGi 9606.ENSP00000366876.

    Chemistry

    BindingDBi Q86YI8.
    ChEMBLi CHEMBL1764945.

    PTM databases

    PhosphoSitei Q86YI8.

    Polymorphism databases

    DMDMi 229462750.

    Proteomic databases

    PaxDbi Q86YI8.
    PRIDEi Q86YI8.

    Protocols and materials databases

    DNASUi 148479.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000377648 ; ENSP00000366876 ; ENSG00000116273 .
    GeneIDi 148479.
    KEGGi hsa:148479.
    UCSCi uc001aob.4. human.

    Organism-specific databases

    CTDi 148479.
    GeneCardsi GC01P006673.
    H-InvDB HIX0000084.
    HGNCi HGNC:22983. PHF13.
    HPAi HPA026830.
    neXtProti NX_Q86YI8.
    PharmGKBi PA134901883.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG281703.
    HOGENOMi HOG000010286.
    HOVERGENi HBG071437.
    InParanoidi Q86YI8.
    OMAi CFGHLQP.
    OrthoDBi EOG7ZKSCH.
    PhylomeDBi Q86YI8.
    TreeFami TF331373.

    Miscellaneous databases

    ChiTaRSi PHF13. human.
    EvolutionaryTracei Q86YI8.
    GenomeRNAii 148479.
    NextBioi 85939.
    PROi Q86YI8.

    Gene expression databases

    Bgeei Q86YI8.
    CleanExi HS_PHF13.
    Genevestigatori Q86YI8.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    Pfami PF00628. PHD. 1 hit.
    [Graphical view ]
    SMARTi SM00249. PHD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF57903. SSF57903. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Testis.
    2. "Homo sapiens protein coding cDNA."
      Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F.
      Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    3. "The DNA sequence and biological annotation of human chromosome 1."
      Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
      , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
      Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLU-20.
      Tissue: Lung and Testis.
    6. Rhodes S., Huckle E.
      Submitted (OCT-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 48-300.
    7. "SPOC1: a novel PHD-containing protein modulating chromatin structure and mitotic chromosome condensation."
      Kinkley S., Staege H., Mohrmann G., Rohaly G., Schaub T., Kremmer E., Winterpacht A., Will H.
      J. Cell Sci. 122:2946-2956(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GSK3B, PROTEASOMAL DEGRADATION, INDUCTION.
    8. "Crystal structure of PHF13 in complex with tri-methylated histone H3K4."
      Structural genomics consortium (SGC)
      Submitted (SEP-2010) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 250-300 IN COMPLEX WITH TRIMETHYLATED HISTONE H3 AND ZINC IONS, X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 232-281.

    Entry informationi

    Entry nameiPHF13_HUMAN
    AccessioniPrimary (citable) accession number: Q86YI8
    Secondary accession number(s): B3KUQ7
    , Q59FB6, Q5TH65, Q8N551, Q9UJP2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 15, 2003
    Last sequence update: May 5, 2009
    Last modified: October 1, 2014
    This is version 96 of the entry and version 2 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 1
      Human chromosome 1: 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3