O04425 (FCA_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Flowering time control protein FCA

Gene names

Name:	FCA
Ordered Locus Names:	At4g16280, At4g16290, At4g16300
ORF Names:	dl4180c, dl4181c, dl4182c, FCAALL.331

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	747 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Plays a major role in the promotion of the transition of the vegetative meristem to reproductive development. Plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. Required for RNA-mediated chromatin silencing of a range of loci in the genome. Cotranscriptionally recognizes aberrant RNA and marks it for silencing. Controls alternative cleavage and polyadenylation on pre-mRNAs and antisense RNAs. Acts redundantly with FPA to prevent the expression of distally polyadenylated antisense RNAs at the FLC locus. Ref.8 Ref.9
Subunit structure	Interacts (via C-terminus) with SWI3B and (via WW domain) with FY (via PPLPP motifs). Ref.5 Ref.6
Subcellular location	Nucleus Ref.7.
Tissue specificity	Constitutively expressed, but the negative feedback maintains the active isoform a low level throughout much of the plant, except in meristematic cells at a specific time in development. Ref.7
Induction	Negative feedback mediated by FCA itself. Ref.7
Domain	The WW domain is required for autoregulation of FCA expression.
Miscellaneous	While FCA requires both FY and FLD, FPA requires FLD but not FY to repress FLC.
Sequence similarities	Contains 2 RRM (RNA recognition motif) domains. Contains 1 WW domain.

Ontologies

Keywords
Biological process	Differentiation Flowering
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	RNA-binding
Molecular function	Developmental protein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW chromatin silencing by small RNA Inferred from mutant phenotype Ref.8. Source: TAIR embryo development Inferred from genetic interaction Ref.8. Source: TAIR embryo sac development Inferred from genetic interaction Ref.8. Source: TAIR flower development Inferred from electronic annotation. Source: UniProtKB-KW regulation of flower development Inferred from mutant phenotype. Source: TAIR
Cellular component	chromatin Traceable author statement Ref.8. Source: TAIR nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	RNA binding Inferred from direct assay Ref.1. Source: TAIR nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform Gamma (identifier: O04425-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Encodes the active protein.

Isoform Alpha (identifier: O04425-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-242: Missing.

Isoform Beta (identifier: O04425-3)

The sequence of this isoform differs from the canonical sequence as follows:
     163-270: CCFVKYATSK...KETAMAAIDG → MSISILLGNS...LDVFEKCRIY
     271-747: Missing.

Isoform Delta (identifier: O04425-4)

The sequence of this isoform differs from the canonical sequence as follows:
     534-747: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 747	747	Flowering time control protein FCA		PRO_0000081588
Regions
	Domain	120 – 201	82	RRM 1
	Domain	211 – 291	81	RRM 2
	Domain	591 – 624	34	WW
	Compositional bias	493 – 558	66	Gln-rich
	Compositional bias	632 – 672	41	Gln-rich
Natural variations
	Alternative sequence	1 – 242	242	Missing in isoform Alpha.		VSP_005794
	Alternative sequence	163 – 270	108	CCFVK…AAIDG → MSISILLGNSRELYFLKFQV SLKRLMGSNPSLIIGLQLFA TIFGLIAYACQRLICVRFCH RRRLPVLRKGLCTYVGQIDF ATCVYSRTLDVFEKCRIY in isoform Beta.		VSP_005795
	Alternative sequence	271 – 747	477	Missing in isoform Beta.		VSP_005796
	Alternative sequence	534 – 747	214	Missing in isoform Delta.		VSP_005797
Experimental info
	Mutagenesis	619	1	W → F: Loss of feedback autoregulation. Ref.6
	Sequence conflict	301	1	E → D in CAB05388. Ref.1
	Sequence conflict	362	1	P → S in CAB05388. Ref.1
	Sequence conflict	362	1	P → S in CAB05389. Ref.1
	Sequence conflict	362	1	P → S in CAB05395. Ref.1
	Sequence conflict	362	1	P → S in AEE83725. Ref.4
	Sequence conflict	732	1	Q → P in CAB05391. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform Gamma [UniParc]. Last modified May 31, 2011. Version 2. Checksum: 32758999E9152FD9	FASTA	747	81,716
	10 20 30 40 50 60 MNGPPDRVDF KPMGPHHGGS FRPMGFAYDD GFRPMGPNGG VGGEGTRSIV GARYNYPAKY 70 80 90 100 110 120 PPSESPDRRR FIGKAMESDY SVRPTTPPVQ QPLSGQKRGY PISDHGSFTG TDVSDRSSTV 130 140 150 160 170 180 KLFVGSVPRT ATEEEIRPYF EQHGNVLEVA LIKDKRTGQQ QGCCFVKYAT SKDADRAIRA 190 200 210 220 230 240 LHNQITLPGG TGPVQVRYAD GERERIGTLE FKLFVGSLNK QATEKEVEEI FLQFGHVEDV 250 260 270 280 290 300 YLMRDEYRQS RGCGFVKYSS KETAMAAIDG LNGTYTMRGC NQPLIVRFAE PKRPKPGESR 310 320 330 340 350 360 EMAPPVGLGS GPRFQASGPR PTSNFGDSSG DVSHTNPWRP ATSRNVGPPS NTGIRGAGSD 370 380 390 400 410 420 FPPKPGQATL PSNQGGPLGG YGVPPLNPLP VPGVSSSATL QQQNRAAGQH ITPLKKPLHS 430 440 450 460 470 480 PQGLPLPLRP QTNFPGAQAP LQNPYAYSSQ LPTSQLPPQQ NISRATAPQT PLNINLRPTT 490 500 510 520 530 540 VSSATVQFPP RSQQQPLQKM QHPPSELAQL LSQQTQSLQA TFQSSQQAIS QLQQQVQSMQ 550 560 570 580 590 600 QPNQNLPLSQ NGRAGKQQWA GSAIPRVAST TGSTPVSYVQ TAAPAVSQSV GSVKCTWTEH 610 620 630 640 650 660 TSPDGFKYYY NGLTGESKWE KPEEMIVFER EQQKQQQHQE KPTIQQSQTQ LQPLQQQPQQ 670 680 690 700 710 720 VQQQYQGQQL QQPFYSSLYP TPGASHNTQY PSLPVGQNSQ FPMSGIGQNA QDYARTHIPV 730 740 GAASMNDISR TQQSRQSPQE LMWKNKA
	Isoform Alpha [UniParc]. Checksum: D2F99EAEF7D364A2	FASTA	505	54,990
	10 20 30 40 50 60 MRDEYRQSRG CGFVKYSSKE TAMAAIDGLN GTYTMRGCNQ PLIVRFAEPK RPKPGESREM 70 80 90 100 110 120 APPVGLGSGP RFQASGPRPT SNFGDSSGDV SHTNPWRPAT SRNVGPPSNT GIRGAGSDFP 130 140 150 160 170 180 PKPGQATLPS NQGGPLGGYG VPPLNPLPVP GVSSSATLQQ QNRAAGQHIT PLKKPLHSPQ 190 200 210 220 230 240 GLPLPLRPQT NFPGAQAPLQ NPYAYSSQLP TSQLPPQQNI SRATAPQTPL NINLRPTTVS 250 260 270 280 290 300 SATVQFPPRS QQQPLQKMQH PPSELAQLLS QQTQSLQATF QSSQQAISQL QQQVQSMQQP 310 320 330 340 350 360 NQNLPLSQNG RAGKQQWAGS AIPRVASTTG STPVSYVQTA APAVSQSVGS VKCTWTEHTS 370 380 390 400 410 420 PDGFKYYYNG LTGESKWEKP EEMIVFEREQ QKQQQHQEKP TIQQSQTQLQ PLQQQPQQVQ 430 440 450 460 470 480 QQYQGQQLQQ PFYSSLYPTP GASHNTQYPS LPVGQNSQFP MSGIGQNAQD YARTHIPVGA 490 500 ASMNDISRTQ QSRQSPQELM WKNKA
	Isoform Beta [UniParc]. Checksum: E09FF175F5DA9694	FASTA	260	29,057
	10 20 30 40 50 60 MNGPPDRVDF KPMGPHHGGS FRPMGFAYDD GFRPMGPNGG VGGEGTRSIV GARYNYPAKY 70 80 90 100 110 120 PPSESPDRRR FIGKAMESDY SVRPTTPPVQ QPLSGQKRGY PISDHGSFTG TDVSDRSSTV 130 140 150 160 170 180 KLFVGSVPRT ATEEEIRPYF EQHGNVLEVA LIKDKRTGQQ QGMSISILLG NSRELYFLKF 190 200 210 220 230 240 QVSLKRLMGS NPSLIIGLQL FATIFGLIAY ACQRLICVRF CHRRRLPVLR KGLCTYVGQI 250 260 DFATCVYSRT LDVFEKCRIY
	Isoform Delta [UniParc]. Checksum: AC5ED9020743F2D3	FASTA	533	57,754
	10 20 30 40 50 60 MNGPPDRVDF KPMGPHHGGS FRPMGFAYDD GFRPMGPNGG VGGEGTRSIV GARYNYPAKY 70 80 90 100 110 120 PPSESPDRRR FIGKAMESDY SVRPTTPPVQ QPLSGQKRGY PISDHGSFTG TDVSDRSSTV 130 140 150 160 170 180 KLFVGSVPRT ATEEEIRPYF EQHGNVLEVA LIKDKRTGQQ QGCCFVKYAT SKDADRAIRA 190 200 210 220 230 240 LHNQITLPGG TGPVQVRYAD GERERIGTLE FKLFVGSLNK QATEKEVEEI FLQFGHVEDV 250 260 270 280 290 300 YLMRDEYRQS RGCGFVKYSS KETAMAAIDG LNGTYTMRGC NQPLIVRFAE PKRPKPGESR 310 320 330 340 350 360 EMAPPVGLGS GPRFQASGPR PTSNFGDSSG DVSHTNPWRP ATSRNVGPPS NTGIRGAGSD 370 380 390 400 410 420 FPPKPGQATL PSNQGGPLGG YGVPPLNPLP VPGVSSSATL QQQNRAAGQH ITPLKKPLHS 430 440 450 460 470 480 PQGLPLPLRP QTNFPGAQAP LQNPYAYSSQ LPTSQLPPQQ NISRATAPQT PLNINLRPTT 490 500 510 520 530 VSSATVQFPP RSQQQPLQKM QHPPSELAQL LSQQTQSLQA TFQSSQQAIS QLQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains." Macknight R., Bancroft I., Page T., Lister C., Schmidt R., Love K., Westphal L., Murphy G., Sherson S., Cobbett C., Dean C. Cell 89:737-745(1997) [PubMed: 9182761] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], ALTERNATIVE SPLICING. Strain: cv. Landsberg erecta.
[2]	"Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana." Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C., Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P., Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E. , Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R., De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M., Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M., Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A., Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D., Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A., Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S., Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G., Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N. Nature 391:485-488(1998) [PubMed: 9461215] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	"Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana." Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B. , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R. Nature 402:769-777(1999) [PubMed: 10617198] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION. Strain: cv. Columbia.
[5]	"AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time." Sarnowski T.J., Swiezewski S., Pawlikowska K., Kaczanowski S., Jerzmanowski A. Nucleic Acids Res. 30:3412-3421(2002) [PubMed: 12140326] [Abstract] Cited for: INTERACTION WITH SWI3B.
[6]	"FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition." Simpson G.G., Dijkwel P.P., Quesada V., Henderson I., Dean C. Cell 113:777-787(2003) [PubMed: 12809608] [Abstract] Cited for: INTERACTION WITH FY, MUTAGENESIS OF TRP-619.
[7]	"Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time." Quesada V., Macknight R., Dean C., Simpson G.G. EMBO J. 22:3142-3152(2003) [PubMed: 12805228] [Abstract] Cited for: INDUCTION BY ITSELF, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[8]	"Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing." Baurle I., Smith L., Baulcombe D.C., Dean C. Science 318:109-112(2007) [PubMed: 17916737] [Abstract] Cited for: FUNCTION.
[9]	"The spen family protein FPA controls alternative cleavage and polyadenylation of RNA." Hornyik C., Terzi L.C., Simpson G.G. Dev. Cell 18:203-213(2010) [PubMed: 20079695] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z82989 mRNA. Translation: CAB05388.1. Z82990 mRNA. Translation: CAB05389.1. Z82991 mRNA. Translation: CAB05390.1. Z82992 Genomic DNA. Translation: CAB05391.1. Z82992 Genomic DNA. Translation: CAB05392.1. Z82992 Genomic DNA. Translation: CAB05393.1. Z82993 mRNA. Translation: CAB05394.1. Z82993 mRNA. Translation: CAB05395.1. Z97340 Genomic DNA. Translation: CAB10407.1. Z97340 Genomic DNA. Translation: CAB46035.1. Z97340 Genomic DNA. Translation: CAB46036.1. AL161543 Genomic DNA. Translation: CAB78670.1. AL161543 Genomic DNA. Translation: CAB78671.1. AL161543 Genomic DNA. Translation: CAB78672.1. CP002687 Genomic DNA. Translation: AEE83725.1. CP002687 Genomic DNA. Translation: AEE83726.1. CP002687 Genomic DNA. Translation: AEE83727.1.
IPI	IPI00527912. IPI00531763. IPI00536196. IPI00544871.
PIR	A85181. B85181. E71429.
RefSeq	NP_193363.4. NM_117725.3. NP_849542.2. NM_179211.2. NP_849543.2. NM_179212.3.
UniGene	At.219.
3D structure databases
ProteinModelPortal	O04425.
SMR	O04425. Positions 119-295, 592-624.
ModBase	Search...
Protein-protein interaction databases
IntAct	O04425. 2 interactions.
STRING	O04425.
Proteomic databases
PRIDE	O04425.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	827323.
GenomeReviews	Gene locus AT4G16280 in contig CT486007_GR.
KEGG	ath:AT4G16280.
Organism-specific databases
TAIR	At4g16280.
Phylogenomic databases
eggNOG	KOG0144.
HOGENOM	HBG633517.
InParanoid	O04425.
PhylomeDB	O04425.
Gene expression databases
Genevestigator	O04425.
Family and domain databases
InterPro	IPR012677. Nucleotide-bd_a/b_plait. IPR000504. RRM_dom. IPR001202. WW_Rsp5_WWP. [Graphical view]
Gene3D	G3DSA:3.30.70.330. a_b_plait_nuc_bd. 2 hits. G3DSA:2.20.70.10. G3DSA:2.20.70.10. 1 hit.
Pfam	PF00076. RRM_1. 2 hits. PF00397. WW. 1 hit. [Graphical view]
SMART	SM00360. RRM. 2 hits. SM00456. WW. 1 hit. [Graphical view]
SUPFAM	SSF51045. WW_Rsp5_WWP. 1 hit.
PROSITE	PS50102. RRM. 2 hits. PS01159. WW_DOMAIN_1. False negative. PS50020. WW_DOMAIN_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

FCA_ARATH

Accession

Primary (citable) accession number: O04425
Secondary accession number(s): F4JLR8 , F4JLR9, O04424, O04727, O23475

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	May 31, 2011
Last modified:	November 16, 2011
This is version 98 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program