PHF6_HUMAN
ID PHF6_HUMAN Reviewed; 365 AA.
AC Q8IWS0; A8K230; B4E0G4; D3DTG3; E9PC97; Q5JRC7; Q5JRC8; Q96JK3; Q9BRU0;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=PHD finger protein 6;
DE AltName: Full=PHD-like zinc finger protein;
GN Name=PHF6; Synonyms=CENP-31, KIAA1823;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, SUBCELLULAR
RP LOCATION, ALTERNATIVE SPLICING, AND VARIANTS BFLS TYR-45; PHE-99; ARG-229;
RP GLU-234 AND GLY-257.
RX PubMed=12415272; DOI=10.1038/ng1040;
RA Lower K.M., Turner G., Kerr B.A., Mathews K.D., Shaw M.A., Gedeon A.K.,
RA Schelley S., Hoyme H.E., White S.M., Delatycki M.B., Lampe A.K.,
RA Clayton-Smith J., Stewart H., van Ravenswaay C.M.A., de Vries B.B.A.,
RA Cox B., Grompe M., Ross S., Thomas P., Mulley J.C., Gecz J.;
RT "Mutations in PHF6 are associated with Boerjeson-Forssman-Lehmann
RT syndrome.";
RL Nat. Genet. 32:661-665(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain;
RX PubMed=11347906; DOI=10.1093/dnares/8.2.85;
RA Nagase T., Nakayama M., Nakajima D., Kikuno R., Ohara O.;
RT "Prediction of the coding sequences of unidentified human genes. XX. The
RT complete sequences of 100 new cDNA clones from brain which code for large
RT proteins in vitro.";
RL DNA Res. 8:85-95(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 4 AND 5).
RC TISSUE=Subthalamic nucleus, and Thymus;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15772651; DOI=10.1038/nature03440;
RA Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D.,
RA Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L.,
RA Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.,
RA Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A.,
RA Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P.,
RA Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D.,
RA Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D.,
RA Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L.,
RA Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P.,
RA Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G.,
RA Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J.,
RA Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D.,
RA Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L.,
RA Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z.,
RA Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S.,
RA Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S.,
RA Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O.,
RA Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H.,
RA Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T.,
RA Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L.,
RA Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R.,
RA Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y.,
RA Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K.,
RA Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J.,
RA Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L.,
RA Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S.,
RA Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A.,
RA Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L.,
RA Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D.,
RA Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H.,
RA McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S.,
RA Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C.,
RA Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S.,
RA Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V.,
RA Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K.,
RA Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K.,
RA Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D.,
RA Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R.,
RA Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B.,
RA Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C.,
RA d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q.,
RA Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N.,
RA Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A.,
RA Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J.,
RA Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A.,
RA Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F.,
RA Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L.,
RA Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S.,
RA Rogers J., Bentley D.R.;
RT "The DNA sequence of the human X chromosome.";
RL Nature 434:325-337(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Bone marrow;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
RA Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.;
RT "Global, in vivo, and site-specific phosphorylation dynamics in signaling
RT networks.";
RL Cell 127:635-648(2006).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-358, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic kidney;
RX PubMed=17525332; DOI=10.1126/science.1140321;
RA Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E.,
RA Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y.,
RA Gygi S.P., Elledge S.J.;
RT "ATM and ATR substrate analysis reveals extensive protein networks
RT responsive to DNA damage.";
RL Science 316:1160-1166(2007).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18691976; DOI=10.1016/j.molcel.2008.07.007;
RA Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R.,
RA Greff Z., Keri G., Stemmann O., Mann M.;
RT "Kinase-selective enrichment enables quantitative phosphoproteomics of the
RT kinome across the cell cycle.";
RL Mol. Cell 31:438-448(2008).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-145,
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146 (ISOFORM 2), AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [13]
RP SUBCELLULAR LOCATION.
RX PubMed=20813266; DOI=10.1016/j.cell.2010.07.047;
RA Ohta S., Bukowski-Wills J.C., Sanchez-Pulido L., Alves Fde L., Wood L.,
RA Chen Z.A., Platani M., Fischer L., Hudson D.F., Ponting C.P., Fukagawa T.,
RA Earnshaw W.C., Rappsilber J.;
RT "The protein composition of mitotic chromosomes determined using
RT multiclassifier combinatorial proteomics.";
RL Cell 142:810-821(2010).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-145, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-155 AND SER-199, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [17]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [18]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH UBTF, AND CHARACTERIZATION
RP OF VARIANTS BFLS TYR-45 AND PHE-99.
RX PubMed=23229552; DOI=10.1074/jbc.m112.414839;
RA Wang J., Leung J.W., Gong Z., Feng L., Shi X., Chen J.;
RT "PHF6 regulates cell cycle progression by suppressing ribosomal RNA
RT synthesis.";
RL J. Biol. Chem. 288:3174-3183(2013).
RN [19]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138; SER-145; SER-155 AND
RP SER-199, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [20]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-173 AND LYS-227, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25218447; DOI=10.1038/nsmb.2890;
RA Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M.,
RA Vertegaal A.C.;
RT "Uncovering global SUMOylation signaling networks in a site-specific
RT manner.";
RL Nat. Struct. Mol. Biol. 21:927-936(2014).
RN [21]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-227, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [22]
RP X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS) OF 208-333, INTERACTION WITH RBBP4,
RP ZINC-FINGERS, EXTENDED PHD DOMAIN, AND DNA-BINDING.
RX PubMed=24554700; DOI=10.1074/jbc.m113.535351;
RA Liu Z., Li F., Ruan K., Zhang J., Mei Y., Wu J., Shi Y.;
RT "Structural and functional insights into the human Borjeson-Forssman-
RT Lehmann syndrome-associated protein PHF6.";
RL J. Biol. Chem. 289:10069-10083(2014).
RN [23]
RP VARIANT BFLS PHE-305.
RX PubMed=23906836; DOI=10.1093/hmg/ddt366;
RA Wieczorek D., Boegershausen N., Beleggia F., Steiner-Haldenstaett S.,
RA Pohl E., Li Y., Milz E., Martin M., Thiele H., Altmueller J., Alanay Y.,
RA Kayserili H., Klein-Hitpass L., Boehringer S., Wollstein A., Albrecht B.,
RA Boduroglu K., Caliebe A., Chrzanowska K., Cogulu O., Cristofoli F.,
RA Czeschik J.C., Devriendt K., Dotti M.T., Elcioglu N., Gener B.,
RA Goecke T.O., Krajewska-Walasek M., Guillen-Navarro E., Hayek J., Houge G.,
RA Kilic E., Simsek-Kiper P.O., Lopez-Gonzalez V., Kuechler A., Lyonnet S.,
RA Mari F., Marozza A., Mathieu Dramard M., Mikat B., Morin G.,
RA Morice-Picard F., Ozkinay F., Rauch A., Renieri A., Tinschert S.,
RA Utine G.E., Vilain C., Vivarelli R., Zweier C., Nuernberg P., Rahmann S.,
RA Vermeesch J., Luedecke H.J., Zeschnigk M., Wollnik B.;
RT "A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser
RT syndromes identifies a broad molecular and clinical spectrum converging on
RT altered chromatin remodeling.";
RL Hum. Mol. Genet. 22:5121-5135(2013).
CC -!- FUNCTION: Transcriptional regulator that associates with ribosomal RNA
CC promoters and suppresses ribosomal RNA (rRNA) transcription.
CC {ECO:0000269|PubMed:23229552}.
CC -!- SUBUNIT: Interacts with UBTF. Interacts with the NuRD complex component
CC RBBP4 (via the nucleolar localization motif), the interaction mediates
CC transcriptional repression activity. {ECO:0000269|PubMed:23229552,
CC ECO:0000269|PubMed:24554700}.
CC -!- SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus. Chromosome,
CC centromere, kinetochore {ECO:0000269|PubMed:20813266}. Note=Nuclear, it
CC particularly localizes to the nucleolus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1; Synonyms=PHF6a, PHF6b;
CC IsoId=Q8IWS0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8IWS0-2; Sequence=VSP_009372, VSP_009373, VSP_009374;
CC Name=3;
CC IsoId=Q8IWS0-3; Sequence=VSP_053441;
CC Name=4;
CC IsoId=Q8IWS0-4; Sequence=VSP_053441, VSP_009373, VSP_009374;
CC Name=5;
CC IsoId=Q8IWS0-5; Sequence=VSP_054937;
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed.
CC {ECO:0000269|PubMed:12415272}.
CC -!- DOMAIN: The PHD-type zinc finger 1 mediates both nucleolar localization
CC and interaction with UBTF.
CC -!- DOMAIN: The ePHD2 domain folds as an integrated structural module
CC comprizing the C2HC pre-PHD-type 2 zinc finger and the PHD-type 2 zinc
CC finger. It mediates non-specific binding to dsDNA, but doesn't bind
CC histones in contrast to many PHD-type zinc fingers.
CC -!- DISEASE: Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900]: An X-
CC linked recessive disorder characterized by moderate to severe
CC intellectual disability, epilepsy, hypogonadism, hypometabolism,
CC obesity with marked gynecomastia, swelling of subcutaneous tissue of
CC the face, narrow palpebral fissure and large but not deformed ears.
CC {ECO:0000269|PubMed:12415272, ECO:0000269|PubMed:23229552,
CC ECO:0000269|PubMed:23906836}. Note=The disease is caused by variants
CC affecting the gene represented in this entry.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB47452.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AY157622; AAO13214.1; -; mRNA.
DR EMBL; AB058726; BAB47452.1; ALT_INIT; mRNA.
DR EMBL; AK290095; BAF82784.1; -; mRNA.
DR EMBL; AK303369; BAG64426.1; -; mRNA.
DR EMBL; AC004383; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL591668; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471107; EAX11762.1; -; Genomic_DNA.
DR EMBL; CH471107; EAX11763.1; -; Genomic_DNA.
DR EMBL; CH471107; EAX11766.1; -; Genomic_DNA.
DR EMBL; BC005994; AAH05994.1; -; mRNA.
DR CCDS; CCDS14639.1; -. [Q8IWS0-1]
DR CCDS; CCDS14640.1; -. [Q8IWS0-2]
DR RefSeq; NP_001015877.1; NM_001015877.1. [Q8IWS0-1]
DR RefSeq; NP_115711.2; NM_032335.3. [Q8IWS0-2]
DR RefSeq; NP_115834.1; NM_032458.2. [Q8IWS0-1]
DR PDB; 4NN2; X-ray; 1.47 A; A/B=208-333.
DR PDB; 4R7A; X-ray; 1.85 A; A=157-171.
DR PDBsum; 4NN2; -.
DR PDBsum; 4R7A; -.
DR AlphaFoldDB; Q8IWS0; -.
DR SMR; Q8IWS0; -.
DR BioGRID; 124022; 272.
DR IntAct; Q8IWS0; 21.
DR MINT; Q8IWS0; -.
DR STRING; 9606.ENSP00000329097; -.
DR GlyGen; Q8IWS0; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q8IWS0; -.
DR PhosphoSitePlus; Q8IWS0; -.
DR SwissPalm; Q8IWS0; -.
DR BioMuta; PHF6; -.
DR DMDM; 42559482; -.
DR EPD; Q8IWS0; -.
DR jPOST; Q8IWS0; -.
DR MassIVE; Q8IWS0; -.
DR MaxQB; Q8IWS0; -.
DR PaxDb; Q8IWS0; -.
DR PeptideAtlas; Q8IWS0; -.
DR PRIDE; Q8IWS0; -.
DR ProteomicsDB; 19401; -.
DR ProteomicsDB; 5670; -.
DR ProteomicsDB; 70885; -. [Q8IWS0-1]
DR ProteomicsDB; 70886; -. [Q8IWS0-2]
DR Antibodypedia; 426; 224 antibodies from 30 providers.
DR DNASU; 84295; -.
DR Ensembl; ENST00000332070.7; ENSP00000329097.3; ENSG00000156531.18. [Q8IWS0-1]
DR Ensembl; ENST00000370800.4; ENSP00000359836.4; ENSG00000156531.18. [Q8IWS0-2]
DR Ensembl; ENST00000370803.8; ENSP00000359839.4; ENSG00000156531.18. [Q8IWS0-1]
DR Ensembl; ENST00000687496.1; ENSP00000509551.1; ENSG00000156531.18. [Q8IWS0-5]
DR Ensembl; ENST00000688598.1; ENSP00000510410.1; ENSG00000156531.18. [Q8IWS0-5]
DR Ensembl; ENST00000691812.1; ENSP00000510211.1; ENSG00000156531.18. [Q8IWS0-1]
DR GeneID; 84295; -.
DR KEGG; hsa:84295; -.
DR MANE-Select; ENST00000370803.8; ENSP00000359839.4; NM_001015877.2; NP_001015877.1.
DR UCSC; uc004exh.4; human. [Q8IWS0-1]
DR CTD; 84295; -.
DR DisGeNET; 84295; -.
DR GeneCards; PHF6; -.
DR HGNC; HGNC:18145; PHF6.
DR HPA; ENSG00000156531; Low tissue specificity.
DR MalaCards; PHF6; -.
DR MIM; 300414; gene.
DR MIM; 301900; phenotype.
DR neXtProt; NX_Q8IWS0; -.
DR OpenTargets; ENSG00000156531; -.
DR Orphanet; 127; Borjeson-Forssman-Lehmann syndrome.
DR PharmGKB; PA33263; -.
DR VEuPathDB; HostDB:ENSG00000156531; -.
DR eggNOG; KOG1084; Eukaryota.
DR GeneTree; ENSGT00950000182865; -.
DR InParanoid; Q8IWS0; -.
DR OMA; RRTYHYH; -.
DR OrthoDB; 783078at2759; -.
DR PhylomeDB; Q8IWS0; -.
DR TreeFam; TF325426; -.
DR PathwayCommons; Q8IWS0; -.
DR SignaLink; Q8IWS0; -.
DR SIGNOR; Q8IWS0; -.
DR BioGRID-ORCS; 84295; 28 hits in 716 CRISPR screens.
DR ChiTaRS; PHF6; human.
DR GeneWiki; PHF6; -.
DR GenomeRNAi; 84295; -.
DR Pharos; Q8IWS0; Tbio.
DR PRO; PR:Q8IWS0; -.
DR Proteomes; UP000005640; Chromosome X.
DR RNAct; Q8IWS0; protein.
DR Bgee; ENSG00000156531; Expressed in corpus epididymis and 195 other tissues.
DR ExpressionAtlas; Q8IWS0; baseline and differential.
DR Genevisible; Q8IWS0; HS.
DR GO; GO:0000776; C:kinetochore; IEA:UniProtKB-KW.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0042393; F:histone binding; IPI:UniProtKB.
DR GO; GO:0042826; F:histone deacetylase binding; IPI:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051219; F:phosphoprotein binding; IPI:UniProtKB.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; IPI:UniProtKB.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0097110; F:scaffold protein binding; IPI:UniProtKB.
DR GO; GO:0015631; F:tubulin binding; IPI:UniProtKB.
DR GO; GO:0001835; P:blastocyst hatching; IEA:Ensembl.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:NTNU_SB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 3.30.40.10; -; 2.
DR IDEAL; IID00594; -.
DR InterPro; IPR034732; EPHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR SMART; SM00249; PHD; 2.
DR PROSITE; PS51805; EPHD; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Centromere; Chromosome;
KW Disease variant; DNA-binding; Epilepsy; Hypotrichosis;
KW Intellectual disability; Isopeptide bond; Kinetochore; Metal-binding;
KW Nucleus; Phosphoprotein; Reference proteome; Repeat; Transcription;
KW Transcription regulation; Ubl conjugation; Zinc; Zinc-finger.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..365
FT /note="PHD finger protein 6"
FT /id="PRO_0000059293"
FT ZN_FING 14..52
FT /note="C2HC pre-PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 80..132
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 209..249
FT /note="C2HC pre-PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 278..330
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 14..132
FT /note="Extended PHD1 domain (ePHD1)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 139..211
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 209..330
FT /note="Extended PHD2 domain (ePHD2)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 330..365
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 13..16
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT MOTIF 129..133
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT MOTIF 157..169
FT /note="Nucleolar localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 139..158
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 182..205
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 330..350
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 351..365
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 138
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163"
FT MOD_RES 145
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163"
FT MOD_RES 155
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21406692,
FT ECO:0007744|PubMed:23186163"
FT MOD_RES 183
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9D4J7"
FT MOD_RES 199
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21406692,
FT ECO:0007744|PubMed:23186163"
FT MOD_RES 358
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17525332"
FT CROSSLNK 173
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25218447"
FT CROSSLNK 227
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25218447,
FT ECO:0007744|PubMed:28112733"
FT VAR_SEQ 47..80
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_054937"
FT VAR_SEQ 140
FT /note="A -> AA (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_009372"
FT VAR_SEQ 140
FT /note="Missing (in isoform 3 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_053441"
FT VAR_SEQ 279..311
FT /note="KCTLCSQPGATIGCEIKACVKTYHYHCGVQDKA -> VCSFYICYATLHLIC
FT CFKFRVHPKFIQSSENLK (in isoform 2 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:14702039,
FT ECO:0000303|PubMed:15489334"
FT /id="VSP_009373"
FT VAR_SEQ 312..365
FT /note="Missing (in isoform 2 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:14702039,
FT ECO:0000303|PubMed:15489334"
FT /id="VSP_009374"
FT VARIANT 45
FT /note="C -> Y (in BFLS; Loss of interaction with UBTF;
FT dbSNP:rs132630299)"
FT /evidence="ECO:0000269|PubMed:12415272,
FT ECO:0000269|PubMed:23229552"
FT /id="VAR_017633"
FT VARIANT 99
FT /note="C -> F (in BFLS; Loss of interaction with UBTF;
FT dbSNP:rs132630298)"
FT /evidence="ECO:0000269|PubMed:12415272,
FT ECO:0000269|PubMed:23229552"
FT /id="VAR_017634"
FT VARIANT 229
FT /note="H -> R (in BFLS; dbSNP:rs104894918)"
FT /evidence="ECO:0000269|PubMed:12415272"
FT /id="VAR_017635"
FT VARIANT 234
FT /note="K -> E (in BFLS; dbSNP:rs104894917)"
FT /evidence="ECO:0000269|PubMed:12415272"
FT /id="VAR_017636"
FT VARIANT 257
FT /note="R -> G (in BFLS; dbSNP:rs104894919)"
FT /evidence="ECO:0000269|PubMed:12415272"
FT /id="VAR_017637"
FT VARIANT 305
FT /note="C -> F (in BFLS; dbSNP:rs587777489)"
FT /evidence="ECO:0000269|PubMed:23906836"
FT /id="VAR_076933"
FT CONFLICT 126
FT /note="V -> A (in Ref. 6; AAH05994)"
FT /evidence="ECO:0000305"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:4NN2"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:4NN2"
FT HELIX 222..225
FT /evidence="ECO:0007829|PDB:4NN2"
FT STRAND 228..230
FT /evidence="ECO:0007829|PDB:4NN2"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:4NN2"
FT HELIX 240..244
FT /evidence="ECO:0007829|PDB:4NN2"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:4NN2"
FT HELIX 265..275
FT /evidence="ECO:0007829|PDB:4NN2"
FT TURN 281..283
FT /evidence="ECO:0007829|PDB:4NN2"
FT STRAND 290..294
FT /evidence="ECO:0007829|PDB:4NN2"
FT HELIX 303..308
FT /evidence="ECO:0007829|PDB:4NN2"
FT STRAND 312..316
FT /evidence="ECO:0007829|PDB:4NN2"
FT TURN 317..320
FT /evidence="ECO:0007829|PDB:4NN2"
FT STRAND 321..325
FT /evidence="ECO:0007829|PDB:4NN2"
FT HELIX 327..329
FT /evidence="ECO:0007829|PDB:4NN2"
FT MOD_RES Q8IWS0-2:146
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648"
SQ SEQUENCE 365 AA; 41290 MW; E8E587909EF9701D CRC64;
MSSSVEQKKG PTRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS ALVSSHSDNE
SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH RTYHYHCALH DKAQIREKPS
QGIYMVYCRK HKKTAHNSEA DLEESFNEHE LEPSSPKSKK KSRKGRPRKT NFKGLSEDTR
STSSHGTDEM ESSSYRDRSP HRSSPSDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY
KCMLFSSGTV QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT
YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGKV EIDQQQLTQQ
QLNGN
