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   05-FEB-2025, entry version 126.
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; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; 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., Pohl T.,
RA   Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA   Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA   de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA   Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA   Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA   Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA   Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA   Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA   Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA   Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA   Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA   Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA   Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA   Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA   Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA   Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA   Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA   Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA   Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA   Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA   Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA   Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA   Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA   de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA   Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA   Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA   Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA   Johnson D., 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., Du H.,
RA   Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA   Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA   Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA   O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA   Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA   Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis 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 reference
RT   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., Hayashizaki Y.,
RA   Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA   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., Hayashizaki Y.,
RA   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 proteins
RT   in the Arabidopsis thaliana genome.";
RL   BMC Genomics 5:39-39(2004).
RN   [6]
RP   HOMODIMER, INTERACTION WITH CPSF30; CLPS3; PCFS5 AND PCFS1, GENE FAMILY,
RP   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., Xing D.,
RA   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 Pcf11p,
RT   regulates FCA alternative processing and promotes flowering 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 of a
RT   polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray.";
RL   PLoS ONE 6:E14719-E14719(2011).
CC   -!- FUNCTION: Promotes flowering by suppressing FLC-mediated inhibition of
CC       flowering through the regulation of FCA pre-mRNA alternative processing
CC       (PubMed:18298670). Regulates mRNA maturation including alternative
CC       polyadenylation, splicing or transcription initiation of stress-
CC       associated genes (PubMed:21364912). {ECO:0000269|PubMed:18298670,
CC       ECO:0000269|PubMed:21364912}.
CC   -!- SUBUNIT: Homodimer. Forms a complex with cleavage and polyadenylation
CC       specificity factor (CPSF) subunits CPSF30, CLPS3 and PCFS1.
CC       {ECO:0000269|PubMed:18298670, ECO:0000269|PubMed:18479511}.
CC   -!- INTERACTION:
CC       Q0WPF2; Q9ZWJ9: ARR2; NbExp=3; IntAct=EBI-1775648, EBI-1101028;
CC       Q0WPF2; Q9LNV5: At1g07360; NbExp=3; IntAct=EBI-1775648, EBI-2430550;
CC       Q0WPF2; C0SUZ3: At1g35490; NbExp=3; IntAct=EBI-1775648, EBI-15192249;
CC       Q0WPF2; Q9SR06: CLPS3; NbExp=3; IntAct=EBI-1775648, EBI-1775627;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18298670}. Cytoplasm
CC       {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 and
CC       flowers. {ECO:0000269|PubMed:18298670}.
CC   -!- DEVELOPMENTAL STAGE: During embryogenesis, first observed at the heart
CC       stage. Expressed through the whole developing embryo from the torpedo
CC       stage. Disappears in the root tip of the mature embryo and in adult
CC       plants. In seedlings, mostly present in the shoot apical meristem and
CC       young leaves. In flowers, detected in sepals, stamens and pistils, but
CC       not in petals. {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 vernalization
CC       treatment. Abnormal alternative polyadenylation-dependent FCA
CC       expression profile of the known transcripts (PubMed:18298670). Global
CC       differentially processed (DPG) and differentially expressed (DEG)
CC       stress-associated genes due to alternative polyadenylation, splicing or
CC       transcription initiation (PubMed:21364912).
CC       {ECO:0000269|PubMed:18298670, 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   AlphaFoldDB; Q0WPF2; -.
DR   SMR; Q0WPF2; -.
DR   BioGRID; 11138; 40.
DR   IntAct; Q0WPF2; 37.
DR   STRING; 3702.Q0WPF2; -.
DR   PaxDb; 3702-AT4G04885.1; -.
DR   ProteomicsDB; 236845; -. [Q0WPF2-1]
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; AT4G04885; PCFS4.
DR   eggNOG; KOG2071; Eukaryota.
DR   HOGENOM; CLU_006062_0_0_1; -.
DR   InParanoid; Q0WPF2; -.
DR   OMA; WPATNSK; -.
DR   OrthoDB; 2129491at2759; -.
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; IEA:InterPro.
DR   GO; GO:0000993; F:RNA polymerase II complex binding; IEA:InterPro.
DR   GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR   GO; GO:0031124; P:mRNA 3'-end processing; IEA:InterPro.
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; IEA:InterPro.
DR   CDD; cd16982; CID_Pcf11; 1.
DR   FunFam; 1.25.40.90:FF:000023; polyadenylation and cleavage factor homolog 4; 1.
DR   Gene3D; 1.25.40.90; -; 1.
DR   InterPro; IPR006569; CID_dom.
DR   InterPro; IPR008942; ENTH_VHS.
DR   InterPro; IPR045154; PCF11-like.
DR   InterPro; IPR047415; Pcf11_CID.
DR   InterPro; IPR013087; Znf_C2H2_type.
DR   PANTHER; PTHR15921:SF12; POLYADENYLATION AND CLEAVAGE FACTOR HOMOLOG 4; 1.
DR   PANTHER; PTHR15921; PRE-MRNA CLEAVAGE COMPLEX II; 1.
DR   Pfam; PF04818; CID; 1.
DR   SMART; SM00582; RPR; 1.
DR   SUPFAM; SSF48464; ENTH/VHS domain; 1.
DR   PROSITE; PS51391; CID; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; Cytoplasm; Flowering; Metal-binding; mRNA processing;
KW   Nucleus; Reference proteome; Zinc; Zinc-finger.
FT   CHAIN           1..808
FT                   /note="Polyadenylation and cleavage factor homolog 4"
FT                   /id="PRO_0000431350"
FT   DOMAIN          61..189
FT                   /note="CID"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00724"
FT   ZN_FING         651..673
FT                   /note="C2H2-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT   REGION          1..32
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          192..212
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          246..293
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          785..808
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        196..205
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        253..263
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        271..280
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   VAR_SEQ         615..808
FT                   /note="Missing (in isoform 2)"
FT                   /id="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
//