PHF6_MOUSE
ID PHF6_MOUSE Reviewed; 364 AA.
AC Q9D4J7; Q80T86; Q8BYT8; Q8C1B5;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=PHD finger protein 6;
GN Name=Phf6; Synonyms=Kiaa1823;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=C57BL/6J; TISSUE=Skin, Testis, and Thymus;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain;
RX PubMed=12693553; DOI=10.1093/dnares/10.1.35;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Aizawa H., Yuasa S.,
RA Nakajima D., Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: II.
RT The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs
RT identified by screening of terminal sequences of cDNA clones randomly
RT sampled from size-fractionated libraries.";
RL DNA Res. 10:35-48(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=C57BL/6J; TISSUE=Brain;
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 [4]
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
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 [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138; SER-145 AND SER-183, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Kidney, Pancreas, and Spleen;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
CC -!- FUNCTION: Transcriptional regulator that associates with ribosomal RNA
CC promoters and suppresses ribosomal RNA (rRNA) transcription.
CC {ECO:0000250}.
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 (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Nucleus, nucleolus
CC {ECO:0000250}. Chromosome, centromere, kinetochore
CC {ECO:0000250|UniProtKB:Q8IWS0}. Note=Nuclear, it particularly localizes
CC to the nucleolus. {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9D4J7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9D4J7-2; Sequence=VSP_009375;
CC -!- TISSUE SPECIFICITY: At 12.5 dpc it is highly expressed in the embryonic
CC central nervous system and at lower levels in other tissues. Very low
CC levels present throughout the adult brain.
CC {ECO:0000269|PubMed:12415272}.
CC -!- DEVELOPMENTAL STAGE: Expression is high in the embryonic and early
CC postnatal stages. {ECO:0000269|PubMed:12415272}.
CC -!- DOMAIN: The PHD-type zinc finger 1 mediates both nucleolar localization
CC and interaction with UBTF. {ECO:0000250}.
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 {ECO:0000250|UniProtKB:Q8IWS0}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC29968.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=BAC65842.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AK016480; BAB30260.1; -; mRNA.
DR EMBL; AK028498; BAC25980.1; -; mRNA.
DR EMBL; AK038320; BAC29968.1; ALT_FRAME; mRNA.
DR EMBL; AK122560; BAC65842.1; ALT_INIT; mRNA.
DR EMBL; BC043127; AAH43127.1; -; mRNA.
DR EMBL; BC055330; AAH55330.1; -; mRNA.
DR EMBL; BC057374; AAH57374.1; -; mRNA.
DR CCDS; CCDS30127.1; -. [Q9D4J7-1]
DR CCDS; CCDS72380.1; -. [Q9D4J7-2]
DR RefSeq; NP_001277475.1; NM_001290546.1. [Q9D4J7-2]
DR RefSeq; NP_081918.1; NM_027642.2. [Q9D4J7-1]
DR AlphaFoldDB; Q9D4J7; -.
DR SMR; Q9D4J7; -.
DR BioGRID; 214404; 4.
DR STRING; 10090.ENSMUSP00000077971; -.
DR iPTMnet; Q9D4J7; -.
DR PhosphoSitePlus; Q9D4J7; -.
DR EPD; Q9D4J7; -.
DR jPOST; Q9D4J7; -.
DR MaxQB; Q9D4J7; -.
DR PaxDb; Q9D4J7; -.
DR PeptideAtlas; Q9D4J7; -.
DR PRIDE; Q9D4J7; -.
DR ProteomicsDB; 288140; -. [Q9D4J7-1]
DR ProteomicsDB; 288141; -. [Q9D4J7-2]
DR Antibodypedia; 426; 224 antibodies from 30 providers.
DR DNASU; 70998; -.
DR Ensembl; ENSMUST00000078944; ENSMUSP00000077971; ENSMUSG00000025626. [Q9D4J7-1]
DR Ensembl; ENSMUST00000154864; ENSMUSP00000130358; ENSMUSG00000025626. [Q9D4J7-2]
DR GeneID; 70998; -.
DR KEGG; mmu:70998; -.
DR UCSC; uc009teo.2; mouse. [Q9D4J7-1]
DR CTD; 84295; -.
DR MGI; MGI:1918248; Phf6.
DR VEuPathDB; HostDB:ENSMUSG00000025626; -.
DR eggNOG; KOG1084; Eukaryota.
DR GeneTree; ENSGT00950000182865; -.
DR HOGENOM; CLU_049182_1_0_1; -.
DR InParanoid; Q9D4J7; -.
DR OMA; RRTYHYH; -.
DR OrthoDB; 783078at2759; -.
DR PhylomeDB; Q9D4J7; -.
DR TreeFam; TF325426; -.
DR BioGRID-ORCS; 70998; 6 hits in 77 CRISPR screens.
DR ChiTaRS; Phf6; mouse.
DR PRO; PR:Q9D4J7; -.
DR Proteomes; UP000000589; Chromosome X.
DR RNAct; Q9D4J7; protein.
DR Bgee; ENSMUSG00000025626; Expressed in manus and 245 other tissues.
DR ExpressionAtlas; Q9D4J7; baseline and differential.
DR Genevisible; Q9D4J7; MM.
DR GO; GO:0000776; C:kinetochore; IEA:UniProtKB-KW.
DR GO; GO:0005730; C:nucleolus; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; IDA:MGI.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0019899; F:enzyme binding; ISO:MGI.
DR GO; GO:0042393; F:histone binding; ISO:MGI.
DR GO; GO:0042826; F:histone deacetylase binding; ISO:MGI.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051219; F:phosphoprotein binding; ISO:MGI.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; ISO:MGI.
DR GO; GO:0097110; F:scaffold protein binding; ISO:MGI.
DR GO; GO:0015631; F:tubulin binding; ISO:MGI.
DR GO; GO:0001835; P:blastocyst hatching; IMP:MGI.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISO:MGI.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 3.30.40.10; -; 2.
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 Acetylation; Alternative splicing; Centromere; Chromosome; DNA-binding;
KW Isopeptide bond; Kinetochore; Metal-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Transcription; Transcription regulation;
KW Ubl conjugation; Zinc; Zinc-finger.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT CHAIN 2..364
FT /note="PHD finger protein 6"
FT /id="PRO_0000059294"
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..364
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..349
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 350..364
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT MOD_RES 138
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 145
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 155
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT MOD_RES 183
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 199
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT MOD_RES 357
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT CROSSLNK 173
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT CROSSLNK 227
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q8IWS0"
FT VAR_SEQ 1..80
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_009375"
SQ SEQUENCE 364 AA; 41139 MW; D147BCE8C553F211 CRC64;
MSSSIEQKKG STRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS ALVSSHSDNE
SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH RTYHYHCALH DKAQIREKPS
QGIYMVYCRK HKKTAHNSEA DLEESFNEHE LEPSSPKTKK KSRKGRPRKT NLKGLPEDSR
STSSHGTDEM ESSSYRDRSP HRSSPNDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY
KCMLFSSGTV QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT
YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGRV AIDQQLTQQQ
LNGN
