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Q86YI8

- PHF13_HUMAN

UniProt

Q86YI8 - PHF13_HUMAN

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Protein

PHD finger protein 13

Gene
PHF13
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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

GO - Cellular componenti

  1. nucleoplasm Source: UniProtKB-SubCell
  2. nucleus Source: UniProtKB
Complete GO annotation...

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.1 Publication

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.

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 signal InferredAdd
BLAST

Sequence similaritiesi

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.

Natural variant

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti111 – 1111K → R in BAG53519. 1 Publication

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 95 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

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