ID   PCFS4_ARATH             Reviewed;         808 AA.
AC   Q0WPF2; Q8GW12; Q9ZS85;
DT   26-NOV-2014, integrated into UniProtKB/Swiss-Prot.
DT   05-SEP-2006, sequence version 1.
DT   31-JUL-2019, entry version 101.
DE   RecName: Full=Polyadenylation and cleavage factor homolog 4 {ECO:0000305};
GN   Name=PCFS4 {ECO:0000303|PubMed:18479511};
GN   OrderedLocusNames=At4g04885 {ECO:0000312|Araport:AT4G04885};
GN   ORFNames=T4B21.1 {ECO:0000312|EMBL:AAD03447.1};
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702 {ECO:0000312|EMBL:BAF00997.1};
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617198; DOI=10.1038/47134;
RA   Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
RA   Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
RA   Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
RA   Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
RA   Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
RA   Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
RA   Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
RA   Langham S.-A., McCullagh B., Bilham L., Robben J.,
RA   van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
RA   Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
RA   Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
RA   Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
RA   De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
RA   van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
RA   Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
RA   Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
RA   Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
RA   Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
RA   Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
RA   Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
RA   Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
RA   Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
RA   Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
RA   Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
RA   Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
RA   Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
RA   Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
RA   Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
RA   Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
RA   Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
RA   Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
RA   Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA   Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA   Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
RA   Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
RA   Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
RA   Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
RA   Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
RA   Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
RA   Chen E., Marra M.A., Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis
RT   thaliana.";
RL   Nature 402:769-777(1999).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana
RT   reference genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   STRAIN=cv. Columbia;
RX   PubMed=11910074; DOI=10.1126/science.1071006;
RA   Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA   Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
RA   Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
RA   Shibata K., Shinagawa A., Shinozaki K.;
RT   "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL   Science 296:141-145(2002).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   STRAIN=cv. Columbia;
RA   Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA   Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA   Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA   Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
RA   Hayashizaki Y., Shinozaki K.;
RT   "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL   Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   GENE FAMILY.
RX   PubMed=15236668; DOI=10.1186/1471-2164-5-39;
RA   Englbrecht C.C., Schoof H., Boehm S.;
RT   "Conservation, diversification and expansion of C2H2 zinc finger
RT   proteins in the Arabidopsis thaliana genome.";
RL   BMC Genomics 5:39-39(2004).
RN   [6]
RP   HOMODIMER, INTERACTION WITH CPSF30; CLPS3; PCFS5 AND PCFS1, GENE
RP   FAMILY, AND NOMENCLATURE.
RX   PubMed=18479511; DOI=10.1186/1471-2164-9-220;
RA   Hunt A.G., Xu R., Addepalli B., Rao S., Forbes K.P., Meeks L.R.,
RA   Xing D., Mo M., Zhao H., Bandyopadhyay A., Dampanaboina L., Marion A.,
RA   Von Lanken C., Li Q.Q.;
RT   "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of
RT   protein-protein interactions and gene expression profiling.";
RL   BMC Genomics 9:220-220(2008).
RN   [7]
RP   FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, INTERACTION WITH
RP   CLPS3, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC   STRAIN=cv. Columbia;
RX   PubMed=18298670; DOI=10.1111/j.1365-313X.2008.03455.x;
RA   Xing D., Zhao H., Xu R., Li Q.Q.;
RT   "Arabidopsis PCFS4, a homologue of yeast polyadenylation factor
RT   Pcf11p, regulates FCA alternative processing and promotes flowering
RT   time.";
RL   Plant J. 54:899-910(2008).
RN   [8]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=cv. Columbia;
RX   PubMed=21364912; DOI=10.1371/journal.pone.0014719;
RA   Zheng J., Xing D., Wu X., Shen Y., Kroll D.M., Ji G., Li Q.Q.;
RT   "Ratio-based analysis of differential mRNA processing and expression
RT   of a polyadenylation factor mutant pcfs4 using arabidopsis tiling
RT   microarray.";
RL   PLoS ONE 6:E14719-E14719(2011).
CC   -!- FUNCTION: Promotes flowering by suppressing FLC-mediated
CC       inhibition of flowering through the regulation of FCA pre-mRNA
CC       alternative processing (PubMed:18298670). Regulates mRNA
CC       maturation including alternative polyadenylation, splicing or
CC       transcription initiation of stress-associated genes
CC       (PubMed:21364912). {ECO:0000269|PubMed:18298670,
CC       ECO:0000269|PubMed:21364912}.
CC   -!- SUBUNIT: Homodimer. Forms a complex with cleavage and
CC       polyadenylation specificity factor (CPSF) subunits CPSF30, CLPS3
CC       and PCFS1. {ECO:0000269|PubMed:18298670,
CC       ECO:0000269|PubMed:18479511}.
CC   -!- INTERACTION:
CC       Q9LNV5:At1g07360; NbExp=3; IntAct=EBI-1775648, EBI-2430550;
CC       C0SUZ3:At1g35490; NbExp=3; IntAct=EBI-1775648, EBI-15192249;
CC       Q9SR06:CLPS3; NbExp=3; IntAct=EBI-1775648, EBI-1775627;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18298670}.
CC       Cytoplasm {ECO:0000269|PubMed:18298670}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q0WPF2-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q0WPF2-2; Sequence=VSP_057255;
CC   -!- TISSUE SPECIFICITY: Expressed in embryos, seedlings, roots, leaves
CC       and flowers. {ECO:0000269|PubMed:18298670}.
CC   -!- DEVELOPMENTAL STAGE: During embryogenesis, first observed at the
CC       heart stage. Expressed through the whole developing embryo from
CC       the torpedo stage. Disappears in the root tip of the mature embryo
CC       and in adult plants. In seedlings, mostly present in the shoot
CC       apical meristem and young leaves. In flowers, detected in sepals,
CC       stamens and pistils, but not in petals.
CC       {ECO:0000269|PubMed:18298670}.
CC   -!- DISRUPTION PHENOTYPE: Delayed flowering mediated by FLC under both
CC       long-day and short-day conditions, but normal response to
CC       vernalization treatment. Abnormal alternative polyadenylation-
CC       dependent FCA expression profile of the known transcripts
CC       (PubMed:18298670). Global differentially processed (DPG) and
CC       differentially expressed (DEG) stress-associated genes due to
CC       alternative polyadenylation, splicing or transcription initiation
CC       (PubMed:21364912). {ECO:0000269|PubMed:18298670,
CC       ECO:0000269|PubMed:21364912}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAD03447.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AF118223; AAD03447.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002687; AEE82437.1; -; Genomic_DNA.
DR   EMBL; AK119152; BAC43722.1; -; mRNA.
DR   EMBL; AK229122; BAF00997.1; -; mRNA.
DR   RefSeq; NP_680598.2; NM_148232.3. [Q0WPF2-1]
DR   SMR; Q0WPF2; -.
DR   BioGrid; 11138; 38.
DR   IntAct; Q0WPF2; 35.
DR   STRING; 3702.AT4G04885.1; -.
DR   PaxDb; Q0WPF2; -.
DR   EnsemblPlants; AT4G04885.1; AT4G04885.1; AT4G04885. [Q0WPF2-1]
DR   GeneID; 825827; -.
DR   Gramene; AT4G04885.1; AT4G04885.1; AT4G04885. [Q0WPF2-1]
DR   KEGG; ath:AT4G04885; -.
DR   Araport; AT4G04885; -.
DR   TAIR; locus:504955249; AT4G04885.
DR   eggNOG; KOG2071; Eukaryota.
DR   eggNOG; ENOG4112CDU; LUCA.
DR   HOGENOM; HOG000242622; -.
DR   InParanoid; Q0WPF2; -.
DR   KO; K14400; -.
DR   OMA; PANNRIF; -.
DR   OrthoDB; 264854at2759; -.
DR   PhylomeDB; Q0WPF2; -.
DR   PRO; PR:Q0WPF2; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; Q0WPF2; baseline and differential.
DR   GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR   GO; GO:0000993; F:RNA polymerase II complex binding; IBA:GO_Central.
DR   GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR   GO; GO:0006378; P:mRNA polyadenylation; IMP:TAIR.
DR   GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR   GO; GO:0009911; P:positive regulation of flower development; IMP:TAIR.
DR   GO; GO:0006369; P:termination of RNA polymerase II transcription; IBA:GO_Central.
DR   Gene3D; 1.25.40.90; -; 1.
DR   InterPro; IPR006569; CID_dom.
DR   InterPro; IPR008942; ENTH_VHS.
DR   InterPro; IPR006903; RNA_pol_II-bd.
DR   InterPro; IPR013087; Znf_C2H2_type.
DR   Pfam; PF04818; CTD_bind; 1.
DR   SMART; SM00582; RPR; 1.
DR   SUPFAM; SSF48464; SSF48464; 1.
DR   PROSITE; PS51391; CID; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; Complete proteome; Cytoplasm; Flowering;
KW   Metal-binding; mRNA processing; Nucleus; Reference proteome; Zinc;
KW   Zinc-finger.
FT   CHAIN         1    808       Polyadenylation and cleavage factor
FT                                homolog 4.
FT                                /FTId=PRO_0000431350.
FT   DOMAIN       61    189       CID. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00724}.
FT   ZN_FING     651    673       C2H2-type. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   VAR_SEQ     615    808       Missing (in isoform 2).
FT                                /FTId=VSP_057255.
SQ   SEQUENCE   808 AA;  89228 MW;  03BABA1EE2B43515 CRC64;
     MDSEKILNPR LVSINSTSRK GMSVELPQKP PPPPSLLDRF KALLNQREDE FGGGEEVLPP
     SMDEIVQLYE VVLGELTFNS KPIITDLTII AGEQREHGEG IANAICTRIL EAPVEQKLPS
     LYLLDSIVKN IGRDYGRYFS SRLPEVFCLA YRQAHPSLHP SMRHLFGTWS SVFPPPVLRK
     IDMQLQLSSA ANQSSVGASE PSQPTRGIHV NPKYLRRLEP SAAENNLRGI NSSARVYGQN
     SLGGYNDFED QLESPSSLSS TPDGFTRRSN DGANPSNQAF NYGMGRATSR DDEHMEWRRK
     ENLGQGNDHE RPRALIDAYG VDTSKHVTIN KPIRDMNGMH SKMVTPWQNT EEEEFDWEDM
     SPTLDRSRAG EFLRSSVPAL GSVRARPRVG NTSDFHLDSD IKNGVSHQLR ENWSLSQNYP
     HTSNRVDTRA GKDLKVLASS VGLVSSNSEF GAPPFDSIQD VNSRFGRALP DGTWPHLSAR
     GPNSLPVPSA HLHHLANPGN AMSNRLQGKP LYRPENQVSQ SHLNDMTQQN QMLVNYLPSS
     SAMAPRPMQS LLTHVSHGYP PHGSTIRPSL SIQGGEAMHP LSSGVLSQIG ASNQPPGGAF
     SGLIGSLMAQ GLISLNNQPA GQGPLGLEFD ADMLKIRNES AISALYGDLP RQCTTCGLRF
     KCQEEHSKHM DWHVTKNRMS KNHKQNPSRK WFVSASMWLS GAEALGAEAV PGFLPTEPTT
     EKKDDEDMAV PADEDQTSCA LCGEPFEDFY SDETEEWMYK GAVYMNAPEE STTDMDKSQL
     GPIVHAKCRP ESNGGDMEEG SQRKKMRS
//