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PHD finger protein 13 (Survival time-associated PHD finger protein in ovarian cancer 1) (SPOC1)

 PHF13_HUMAN             Reviewed;         300 AA.
Q86YI8; B3KUQ7; Q59FB6; Q5TH65; Q8N551; Q9UJP2;
15-AUG-2003, integrated into UniProtKB/Swiss-Prot.
05-MAY-2009, sequence version 2.
25-APR-2018, entry version 121.
RecName: Full=PHD finger protein 13;
AltName: Full=Survival time-associated PHD finger protein in ovarian cancer 1;
Short=SPOC1;
Name=PHF13;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Testis;
PubMed=14702039; DOI=10.1038/ng1285;
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.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Brain;
Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.,
Ohara O., Nagase T., Kikuno R.F.;
"Homo sapiens protein coding cDNA.";
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
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.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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., 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.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT GLU-20.
TISSUE=Lung, and Testis;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 48-300.
Rhodes S., Huckle E.;
Submitted (OCT-1999) to the EMBL/GenBank/DDBJ databases.
[7]
FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GSK3B, PROTEASOMAL
DEGRADATION, AND INDUCTION.
PubMed=19638409; DOI=10.1242/jcs.047365;
Kinkley S., Staege H., Mohrmann G., Rohaly G., Schaub T., Kremmer E.,
Winterpacht A., Will H.;
"SPOC1: a novel PHD-containing protein modulating chromatin structure
and mitotic chromosome condensation.";
J. Cell Sci. 122:2946-2956(2009).
[8]
X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 250-300 IN COMPLEX WITH
TRIMETHYLATED HISTONE H3 AND ZINC IONS, AND X-RAY CRYSTALLOGRAPHY
(1.85 ANGSTROMS) OF 232-281.
Structural genomics consortium (SGC);
"Crystal structure of PHF13 in complex with tri-methylated histone
H3K4.";
Submitted (SEP-2010) to the PDB data bank.
-!- FUNCTION: Modulates chromatin structure. Required for normal
chromosome condensation during the early stages of mitosis.
Required for normal chromosome separation during mitosis.
{ECO:0000269|PubMed:19638409}.
-!- SUBUNIT: Interacts with histone H3 that is trimethylated at 'Lys-
4' (H3K4me3). Interacts with GSK3B. {ECO:0000269|PubMed:19638409,
ECO:0000269|Ref.8}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19638409}.
Nucleus, nucleoplasm {ECO:0000269|PubMed:19638409}.
Note=Predominantly bound to chromatin, but a minor proportion is
also detected in the nucleoplasm.
-!- 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. {ECO:0000269|PubMed:19638409}.
-!- PTM: Subject to proteasomal degradation. Stable when bound to
chromatin. The soluble form is rapidly degraded.
-!- SEQUENCE CAUTION:
Sequence=AAH32792.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
Sequence=BAD92781.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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EMBL; AK315110; BAG37568.1; -; mRNA.
EMBL; AK097715; BAG53519.1; -; mRNA.
EMBL; AB209544; BAD92781.1; ALT_INIT; mRNA.
EMBL; AL031447; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CH471130; EAW71561.1; -; Genomic_DNA.
EMBL; BC032792; AAH32792.2; ALT_INIT; mRNA.
EMBL; BC038516; AAH38516.1; -; mRNA.
EMBL; AL121733; CAB57324.1; -; mRNA.
CCDS; CCDS85.1; -.
RefSeq; NP_722519.2; NM_153812.2.
UniGene; Hs.516079; -.
PDB; 3O70; X-ray; 1.85 A; A=232-281.
PDB; 3O7A; X-ray; 1.67 A; A=229-280.
PDBsum; 3O70; -.
PDBsum; 3O7A; -.
ProteinModelPortal; Q86YI8; -.
SMR; Q86YI8; -.
BioGrid; 127151; 4.
IntAct; Q86YI8; 1.
BindingDB; Q86YI8; -.
ChEMBL; CHEMBL1764945; -.
iPTMnet; Q86YI8; -.
PhosphoSitePlus; Q86YI8; -.
BioMuta; PHF13; -.
DMDM; 229462750; -.
EPD; Q86YI8; -.
PaxDb; Q86YI8; -.
PeptideAtlas; Q86YI8; -.
PRIDE; Q86YI8; -.
DNASU; 148479; -.
Ensembl; ENST00000377648; ENSP00000366876; ENSG00000116273.
GeneID; 148479; -.
KEGG; hsa:148479; -.
UCSC; uc001aob.5; human.
CTD; 148479; -.
DisGeNET; 148479; -.
EuPathDB; HostDB:ENSG00000116273.5; -.
GeneCards; PHF13; -.
H-InvDB; HIX0000084; -.
HGNC; HGNC:22983; PHF13.
HPA; HPA026830; -.
neXtProt; NX_Q86YI8; -.
OpenTargets; ENSG00000116273; -.
PharmGKB; PA134901883; -.
eggNOG; ENOG410IMXF; Eukaryota.
eggNOG; ENOG4111YY1; LUCA.
GeneTree; ENSGT00530000063882; -.
HOGENOM; HOG000010286; -.
HOVERGEN; HBG071437; -.
InParanoid; Q86YI8; -.
OMA; CFGHLQP; -.
OrthoDB; EOG091G0FTQ; -.
PhylomeDB; Q86YI8; -.
TreeFam; TF331373; -.
ChiTaRS; PHF13; human.
EvolutionaryTrace; Q86YI8; -.
GenomeRNAi; 148479; -.
PRO; PR:Q86YI8; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000116273; -.
CleanEx; HS_PHF13; -.
ExpressionAtlas; Q86YI8; baseline and differential.
Genevisible; Q86YI8; HS.
GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0035064; F:methylated histone binding; NAS:UniProtKB.
GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
GO; GO:0007059; P:chromosome segregation; IMP:UniProtKB.
GO; GO:0000278; P:mitotic cell cycle; IMP:UniProtKB.
GO; GO:0007076; P:mitotic chromosome condensation; IMP:UniProtKB.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR019787; Znf_PHD-finger.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF00628; PHD; 1.
SMART; SM00249; PHD; 1.
SUPFAM; SSF57903; SSF57903; 1.
1: Evidence at protein level;
3D-structure; Cell cycle; Cell division; Chromatin regulator;
Complete proteome; DNA condensation; Metal-binding; Mitosis; Nucleus;
Polymorphism; Reference proteome; Zinc; Zinc-finger.
CHAIN 1 300 PHD finger protein 13.
/FTId=PRO_0000059304.
ZN_FING 232 280 PHD-type.
REGION 241 248 Interaction with trimethylated histone H3
(H3K4).
MOTIF 110 127 Nuclear localization signal.
{ECO:0000305}.
VARIANT 20 20 K -> E (in dbSNP:rs17853850).
{ECO:0000269|PubMed:15489334}.
/FTId=VAR_055285.
CONFLICT 111 111 K -> R (in Ref. 1; BAG53519).
{ECO:0000305}.
STRAND 246 248 {ECO:0000244|PDB:3O7A}.
TURN 250 252 {ECO:0000244|PDB:3O7A}.
STRAND 255 257 {ECO:0000244|PDB:3O7A}.
TURN 258 262 {ECO:0000244|PDB:3O7A}.
HELIX 265 267 {ECO:0000244|PDB:3O7A}.
HELIX 275 278 {ECO:0000244|PDB:3O7A}.
SEQUENCE 300 AA; 33582 MW; 197663A113B995F2 CRC64;
MDSDSCAAAF HPEEYSPSCK RRRTVEDFNK FCTFVLAYAG YIPYPKEELP LRSSPSPANS
TAGTIDSDGW DAGFSDIASS VPLPVSDRCF SHLQPTLLQR AKPSNFLLDR KKTDKLKKKK
KRKRRDSDAP GKEGYRGGLL KLEAADPYVE TPTSPTLQDI PQAPSDPCSG WDSDTPSSGS
CATVSPDQVK EIKTEGKRTI VRQGKQVVFR DEDSTGNDED IMVDSDDDSW DLVTCFCMKP
FAGRPMIECN ECHTWIHLSC AKIRKSNVPE VFVCQKCRDS KFDIRRSNRS RTGSRKLFLD


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