FCA_ORYSJ
ID FCA_ORYSJ Reviewed; 738 AA.
AC Q6K271; A0A0P0XKM4; Q0J3F0; Q6VQR2; Q6W5F4; Q6W5F5; Q6WQT6;
DT 05-JUN-2019, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Flowering time control protein FCA {ECO:0000303|PubMed:16240176, ECO:0000303|Ref.1};
DE Short=OsFCA {ECO:0000303|PubMed:16753815};
DE Short=rFCA {ECO:0000303|PubMed:17597396};
GN Name=FCA {ECO:0000303|PubMed:16240176, ECO:0000303|PubMed:16753815,
GN ECO:0000303|Ref.1};
GN OrderedLocusNames=LOC_Os09g03610 {ECO:0000305},
GN Os09g0123200 {ECO:0000312|EMBL:BAT06887.1};
GN ORFNames=OSNPB_090123200 {ECO:0000312|EMBL:BAT06887.1},
GN P0415D04.46-1 {ECO:0000312|EMBL:BAD20100.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Winichayakul S., Beswick N., Macknight R.;
RT "Components of the Arabidopsis autonomous floral promotion pathway, FCA and
RT FY, are conserved in grasses.";
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, ALTERNATIVE SPLICING,
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Ilpoom; TISSUE=Seedling;
RX PubMed=16240176; DOI=10.1007/s11103-005-8105-8;
RA Lee J.-H., Cho Y.-S., Yoon H.-S., Suh M.C., Moon J., Lee I., Weigel D.,
RA Yun C.-H., Kim J.-K.;
RT "Conservation and divergence of FCA function between Arabidopsis and
RT rice.";
RL Plant Mol. Biol. 58:823-838(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4), ALTERNATIVE SPLICING,
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Wuyunjing 7; TISSUE=Callus, and Leaf;
RX PubMed=16753815; DOI=10.1080/10425170500136707;
RA Du X., Qian X., Wang D., Yang J.;
RT "Alternative splicing and expression analysis of OsFCA (FCA in Oryza sativa
RT L.), a gene homologous to FCA in Arabidopsis.";
RL DNA Seq. 17:31-40(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP INTERACTION WITH FY.
RX PubMed=16820865; DOI=10.1111/j.1745-7270.2006.00188.x;
RA Lu Q., Xu Z.-K., Song R.-T.;
RT "OsFY, a homolog of AtFY, encodes a protein that can interact with OsFCA-
RT gamma in rice (Oryza sativa L.).";
RL Acta Biochim. Biophys. Sin. 38:492-499(2006).
RN [7]
RP FUNCTION.
RC STRAIN=cv. Zhonghua 11;
RX PubMed=17597396; DOI=10.1007/s10540-007-9047-y;
RA Hong F., Attia K., Wei C., Li K., He G., Su W., Zhang Q., Qian X., Yang J.;
RT "Overexpression of the rFCA RNA recognition motif affects morphologies
RT modifications in rice (Oryza sativa L.).";
RL Biosci. Rep. 27:225-234(2007).
RN [8]
RP INTERACTION WITH FY.
RX PubMed=18854333; DOI=10.1093/pcp/pcn151;
RA Jang Y.H., Lee J.H., Kim J.K.;
RT "Abscisic acid does not disrupt either the Arabidopsis FCA-FY interaction
RT or its rice counterpart in vitro.";
RL Plant Cell Physiol. 49:1898-1901(2008).
RN [9]
RP INTERACTION WITH FY; SF1; FIK; RPRD1B; OS09G0509000/LOC_OS09G33480 AND
RP MADS8, TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=19561057; DOI=10.1093/pcp/pcp093;
RA Jang Y.H., Park H.-Y., Kim S.-K., Lee J.H., Suh M.C., Chung Y.S.,
RA Paek K.-H., Kim J.-K.;
RT "Survey of rice proteins interacting with OsFCA and OsFY proteins which are
RT homologous to the Arabidopsis flowering time proteins, FCA and FY.";
RL Plant Cell Physiol. 50:1479-1492(2009).
CC -!- FUNCTION: Plays a major role in the promotion of the transition of the
CC vegetative meristem to reproductive development (PubMed:16240176).
CC Required for RNA-mediated chromatin silencing of a range of loci in the
CC genome. Cotranscriptionally recognizes aberrant RNA and marks it for
CC silencing. Controls alternative cleavage and polyadenylation on pre-
CC mRNAs and antisense RNAs (By similarity). Regulates flowering time,
CC seed size and cell volume, probably via the modulation of cell size
CC (PubMed:17597396). {ECO:0000250|UniProtKB:O04425,
CC ECO:0000269|PubMed:16240176, ECO:0000269|PubMed:17597396}.
CC -!- SUBUNIT: Interacts with FY (PubMed:16820865, PubMed:18854333,
CC PubMed:19561057). Binds to SF1, FIK, RPRD1B,
CC Os09g0509000/LOC_Os09g33480 and MADS8 (PubMed:19561057).
CC {ECO:0000269|PubMed:16820865, ECO:0000269|PubMed:18854333,
CC ECO:0000269|PubMed:19561057}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19561057}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Comment=Additional isoforms alpha and beta seem to exist.
CC {ECO:0000269|PubMed:16240176};
CC Name=1; Synonyms=gamma {ECO:0000303|PubMed:16240176,
CC ECO:0000303|PubMed:16753815}, OsFCA-1 {ECO:0000303|PubMed:16753815};
CC IsoId=Q6K271-1; Sequence=Displayed;
CC Name=2; Synonyms=OsFCA-3 {ECO:0000303|PubMed:16753815};
CC IsoId=Q6K271-2; Sequence=VSP_060184;
CC Name=3; Synonyms=OsFCA-2 {ECO:0000303|PubMed:16753815};
CC IsoId=Q6K271-3; Sequence=VSP_060185, VSP_060186;
CC Name=4; Synonyms=OsFCA-4 {ECO:0000303|PubMed:16753815};
CC IsoId=Q6K271-4; Sequence=VSP_060184, VSP_060187;
CC -!- TISSUE SPECIFICITY: Mostly expressed in young flowers (panicles) and
CC stems, and also present in young seedlings leaves and roots.
CC {ECO:0000269|PubMed:16240176, ECO:0000269|PubMed:16753815,
CC ECO:0000269|PubMed:19561057}.
CC -!- DEVELOPMENTAL STAGE: Mainly observed at earlier stages of panicle
CC development (PubMed:16240176). Up-regulated in young spikelet of
CC primary branch-differentiating stage and down-regulated in young
CC spikelet of pistil and stamen-differentiating stage (PubMed:16753815).
CC Accumulates in differentiating calli (PubMed:16753815).
CC {ECO:0000269|PubMed:16240176, ECO:0000269|PubMed:16753815}.
CC -!- MISCELLANEOUS: [Isoform 1]: Major isoform.
CC {ECO:0000269|PubMed:16753815}.
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DR EMBL; AY654584; AAT72462.1; -; mRNA.
DR EMBL; AY730687; AAW62371.1; -; mRNA.
DR EMBL; AY274928; AAQ17123.1; -; mRNA.
DR EMBL; AY311343; AAQ74971.1; -; mRNA.
DR EMBL; AY311344; AAQ74972.1; -; mRNA.
DR EMBL; AY331574; AAQ74973.1; -; mRNA.
DR EMBL; AP008215; BAF24515.1; -; Genomic_DNA.
DR EMBL; AP006062; BAD20100.1; -; Genomic_DNA.
DR EMBL; AP014965; BAT06887.1; -; Genomic_DNA.
DR EMBL; AP014965; BAT06888.1; -; Genomic_DNA.
DR RefSeq; XP_015612120.1; XM_015756634.1. [Q6K271-1]
DR AlphaFoldDB; Q6K271; -.
DR SMR; Q6K271; -.
DR STRING; 4530.OS09T0123200-01; -.
DR PaxDb; Q6K271; -.
DR PRIDE; Q6K271; -.
DR EnsemblPlants; Os09t0123200-01; Os09t0123200-01; Os09g0123200. [Q6K271-1]
DR EnsemblPlants; Os09t0123200-02; Os09t0123200-02; Os09g0123200.
DR GeneID; 4346429; -.
DR Gramene; Os09t0123200-01; Os09t0123200-01; Os09g0123200. [Q6K271-1]
DR Gramene; Os09t0123200-02; Os09t0123200-02; Os09g0123200.
DR eggNOG; KOG0144; Eukaryota.
DR HOGENOM; CLU_020343_0_0_1; -.
DR InParanoid; Q6K271; -.
DR OMA; FHPYRGP; -.
DR OrthoDB; 1209165at2759; -.
DR Proteomes; UP000000763; Chromosome 9.
DR Proteomes; UP000059680; Chromosome 9.
DR ExpressionAtlas; Q6K271; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005681; C:spliceosomal complex; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0048026; P:positive regulation of mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0008361; P:regulation of cell size; IMP:UniProtKB.
DR GO; GO:0009909; P:regulation of flower development; IMP:UniProtKB.
DR GO; GO:0080113; P:regulation of seed growth; IMP:UniProtKB.
DR GO; GO:0048510; P:regulation of timing of transition from vegetative to reproductive phase; IMP:UniProtKB.
DR CDD; cd00201; WW; 1.
DR Gene3D; 3.30.70.330; -; 2.
DR InterPro; IPR002343; Hud_Sxl_RNA.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR001202; WW_dom.
DR InterPro; IPR036020; WW_dom_sf.
DR Pfam; PF00076; RRM_1; 2.
DR Pfam; PF00397; WW; 1.
DR PRINTS; PR00961; HUDSXLRNA.
DR SMART; SM00360; RRM; 2.
DR SMART; SM00456; WW; 1.
DR SUPFAM; SSF51045; SSF51045; 1.
DR SUPFAM; SSF54928; SSF54928; 2.
DR PROSITE; PS50102; RRM; 2.
DR PROSITE; PS50020; WW_DOMAIN_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Developmental protein; Differentiation; Flowering;
KW Nucleus; Reference proteome; Repeat; RNA-binding.
FT CHAIN 1..738
FT /note="Flowering time control protein FCA"
FT /id="PRO_0000447371"
FT DOMAIN 122..203
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 213..293
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 609..642
FT /note="WW"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT REGION 1..118
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 292..414
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 566..594
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 670..738
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 345..404
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..102
FT /note="MHRGGDRSTDPSSGPAPGSRGGGDGRFGRGPSRWSSGGGGGGSGSPPHRFSR
FT GGGGGGGDGGGGGGGGGRFHPYRGPSDHSGGGGYRSGGGGEYGEPGSGPR -> M (in
FT isoform 2 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:16753815"
FT /id="VSP_060184"
FT VAR_SEQ 578..649
FT /note="GQPVQSSNPGAPNAIIPSNINTIPQQATSPAVPLTCNWTEHTSPEGFKYYYN
FT SITRESKWDKPEEYVLYEQQ -> VAEQHVFSMHTPMCTRFVFSCIMWFTADIFFNRFC
FT FHYRVSQCNLVTLVPQMPLFHQTLIQFPSRLLHLQFL (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16753815"
FT /id="VSP_060185"
FT VAR_SEQ 650..738
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16753815"
FT /id="VSP_060186"
FT VAR_SEQ 728..738
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:16753815"
FT /id="VSP_060187"
FT CONFLICT 441
FT /note="L -> Q (in Ref. 3; AAQ74973)"
FT /evidence="ECO:0000305"
FT CONFLICT 727
FT /note="G -> N (in Ref. 3; AAQ74973)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 738 AA; 79658 MW; 3ABBCCB87D237C25 CRC64;
MHRGGDRSTD PSSGPAPGSR GGGDGRFGRG PSRWSSGGGG GGSGSPPHRF SRGGGGGGGD
GGGGGGGGGR FHPYRGPSDH SGGGGYRSGG GGEYGEPGSG PRHRYGSGRG DHSDHDNRNN
YVKLFIGSVP RTATEDDVRP LFEEHGDVVE VALIKDRKTG EQQGCCFVKY ATSEEAERAI
RALHNQYTLP GAMGPIQVRY ADGERERHGA IEHKLFVASL NKQATAKEIE EIFAPYGHVE
DVYIMKDGMR QSRGCGFVKF SSREPALAAM SALSGNYVMR GCEQPLIIRF ADPKRPRPGE
SRGGPAFGGP GFSPRSDAAL VIRPTANLDE PRGRHMPPDS WHPSSPRSAP HQFNNFGSDN
PMAPKGSTVT STTDTATFRP QMFSGNGSLS SQTAVPSSSH MGMNPPPMAQ GHHLGGQQIP
PLQKLPGLPQ NFPVQLQNNQ LGQPLQGPAQ QIGQLQVPQS MGPGSFGQNR LSGQLPVSQP
LMQQNASVSA VQVPSAVSNS MQAIPGQQHL PSNVAPQMLQ QPVQQMPSQA PQLLLQQQAA
LQSSYQSSQQ AIYQLQQQLQ LMQQQQQSNL NHQQPTQGQP VQSSNPGAPN AIIPSNINTI
PQQATSPAVP LTCNWTEHTS PEGFKYYYNS ITRESKWDKP EEYVLYEQQQ QQQQQQKLLL
LQQHQQKLAM QQLQSPPQAQ THPAMQPVQQ IPQAQQGQQQ MQMKQQELNY TQLQTPGAID
PSRIQQGIQS AQERAWKS
