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Q86YI8 (PHF13_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
PHD finger protein 13
Alternative name(s):
Survival time-associated PHD finger protein in ovarian cancer 1
Short name=SPOC1
Gene names
Name:PHF13
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length300 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis. Ref.7

Subunit structure

Interacts with histone H3 that is trimethylated at 'Lys-4' (H3K4me3). Interacts with GSK3B. Ref.7

Subcellular location

Nucleus. Nucleusnucleoplasm. Note: Predominantly bound to chromatin, but a minor proportion is also detected in the nucleoplasm. Ref.7

Induction

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. Ref.7

Post-translational modification

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

Sequence similarities

Contains 1 PHD-type zinc finger.

Sequence caution

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 300300PHD finger protein 13
PRO_0000059304

Regions

Zinc finger232 – 28049PHD-type
Region241 – 2488Interaction with trimethylated histone H3 (H3K4)
Motif110 – 12718Nuclear localization signal Probable

Natural variations

Natural variant201K → E. Ref.5
Corresponds to variant rs17853850 [ dbSNP | Ensembl ].
VAR_055285

Experimental info

Sequence conflict1111K → R in BAG53519. Ref.1

Secondary structure

............ 300
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q86YI8 [UniParc].

Last modified May 5, 2009. Version 2.
Checksum: 197663A113B995F2

FASTA30033,582
        10         20         30         40         50         60 
MDSDSCAAAF HPEEYSPSCK RRRTVEDFNK FCTFVLAYAG YIPYPKEELP LRSSPSPANS 

        70         80         90        100        110        120 
TAGTIDSDGW DAGFSDIASS VPLPVSDRCF SHLQPTLLQR AKPSNFLLDR KKTDKLKKKK 

       130        140        150        160        170        180 
KRKRRDSDAP GKEGYRGGLL KLEAADPYVE TPTSPTLQDI PQAPSDPCSG WDSDTPSSGS 

       190        200        210        220        230        240 
CATVSPDQVK EIKTEGKRTI VRQGKQVVFR DEDSTGNDED IMVDSDDDSW DLVTCFCMKP 

       250        260        270        280        290        300 
FAGRPMIECN ECHTWIHLSC AKIRKSNVPE VFVCQKCRDS KFDIRRSNRS RTGSRKLFLD 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_722519.2. NM_153812.2.
UniGeneHs.516079.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3O70X-ray1.85A232-281[»]
3O7AX-ray1.67A229-280[»]
ProteinModelPortalQ86YI8.
SMRQ86YI8. Positions 229-280.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid127151. 1 interaction.
IntActQ86YI8. 1 interaction.
STRING9606.ENSP00000366876.

Chemistry

BindingDBQ86YI8.
ChEMBLCHEMBL1764945.

PTM databases

PhosphoSiteQ86YI8.

Polymorphism databases

DMDM229462750.

Proteomic databases

PaxDbQ86YI8.
PRIDEQ86YI8.

Protocols and materials databases

DNASU148479.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000377648; ENSP00000366876; ENSG00000116273.
GeneID148479.
KEGGhsa:148479.
UCSCuc001aob.4. human.

Organism-specific databases

CTD148479.
GeneCardsGC01P006673.
H-InvDBHIX0000084.
HGNCHGNC:22983. PHF13.
HPAHPA026830.
neXtProtNX_Q86YI8.
PharmGKBPA134901883.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG281703.
HOGENOMHOG000010286.
HOVERGENHBG071437.
InParanoidQ86YI8.
OMAGDPCSGW.
OrthoDBEOG7ZKSCH.
PhylomeDBQ86YI8.
TreeFamTF331373.

Gene expression databases

BgeeQ86YI8.
CleanExHS_PHF13.
GenevestigatorQ86YI8.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamPF00628. PHD. 1 hit.
[Graphical view]
SMARTSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
ProtoNetSearch...

Other

ChiTaRSPHF13. human.
EvolutionaryTraceQ86YI8.
GenomeRNAi148479.
NextBio85939.
PROQ86YI8.

Entry information

Entry namePHF13_HUMAN
AccessionPrimary (citable) accession number: Q86YI8
Secondary accession number(s): B3KUQ7 expand/collapse secondary AC list , Q59FB6, Q5TH65, Q8N551, Q9UJP2
Entry history
Integrated into UniProtKB/Swiss-Prot: August 15, 2003
Last sequence update: May 5, 2009
Last modified: April 16, 2014
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM