RS40_ARATH
ID RS40_ARATH Reviewed; 350 AA.
AC P92965; A8MRZ9; B9DH58; F4JSN1; Q96333;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 2.
DT 25-MAY-2022, entry version 163.
DE RecName: Full=Serine/arginine-rich splicing factor RS40;
DE Short=At-RSp40;
DE Short=AtRS40;
GN Name=RS40; Synonyms=RSP35, RSP40; OrderedLocusNames=At4g25500;
GN ORFNames=M7J2.130;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=8989882; DOI=10.2307/3870466;
RA Lopato S., Waigmann E., Barta A.;
RT "Characterization of a novel arginine/serine-rich splicing factor in
RT Arabidopsis.";
RL Plant Cell 8:2255-2264(1996).
RN [2]
RP SEQUENCE REVISION.
RA Barta A.;
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RA Wintz H., Sakamoto W.;
RL Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [5]
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 [6]
RP SUBCELLULAR LOCATION.
RX PubMed=15133128; DOI=10.1091/mbc.e04-01-0055;
RA Lorkovic Z.J., Hilscher J., Barta A.;
RT "Use of fluorescent protein tags to study nuclear organization of the
RT spliceosomal machinery in transiently transformed living plant cells.";
RL Mol. Biol. Cell 15:3233-3243(2004).
RN [7]
RP INTERACTION WITH SNRNP35.
RX PubMed=15987817; DOI=10.1261/rna.2440305;
RA Lorkovic Z.J., Lehner R., Forstner C., Barta A.;
RT "Evolutionary conservation of minor U12-type spliceosome between plants and
RT humans.";
RL RNA 11:1095-1107(2005).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [9]
RP ALTERNATIVE SPLICING.
RX PubMed=16520337; DOI=10.1093/molbev/msj118;
RA Iida K., Go M.;
RT "Survey of conserved alternative splicing events of mRNAs encoding SR
RT proteins in land plants.";
RL Mol. Biol. Evol. 23:1085-1094(2006).
RN [10]
RP ALTERNATIVE SPLICING, AND TISSUE SPECIFICITY.
RX PubMed=16936312; DOI=10.1093/nar/gkl570;
RA Kalyna M., Lopato S., Voronin V., Barta A.;
RT "Evolutionary conservation and regulation of particular alternative
RT splicing events in plant SR proteins.";
RL Nucleic Acids Res. 34:4395-4405(2006).
RN [11]
RP INTERACTION WITH CYP59.
RX PubMed=16497658; DOI=10.1261/rna.2226106;
RA Gullerova M., Barta A., Lorkovic Z.J.;
RT "AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that
RT interacts with SR proteins and the C-terminal domain of the RNA polymerase
RT II.";
RL RNA 12:631-643(2006).
RN [12]
RP ALTERNATIVE SPLICING, AND INDUCTION.
RX PubMed=17319848; DOI=10.1111/j.1365-313x.2006.03020.x;
RA Palusa S.G., Ali G.S., Reddy A.S.;
RT "Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich
RT proteins: regulation by hormones and stresses.";
RL Plant J. 49:1091-1107(2007).
RN [13]
RP SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-298,
RP AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211; SER-262 AND SER-298, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [15]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=20884799; DOI=10.1105/tpc.110.078352;
RA Barta A., Kalyna M., Reddy A.S.;
RT "Implementing a rational and consistent nomenclature for serine/arginine-
RT rich protein splicing factors (SR proteins) in plants.";
RL Plant Cell 22:2926-2929(2010).
RN [16]
RP GENE FAMILY.
RX PubMed=21935421; DOI=10.1371/journal.pone.0024542;
RA Richardson D.N., Rogers M.F., Labadorf A., Ben-Hur A., Guo H.,
RA Paterson A.H., Reddy A.S.N.;
RT "Comparative analysis of serine/arginine-rich proteins across 27
RT eukaryotes: insights into sub-family classification and extent of
RT alternative splicing.";
RL PLoS ONE 6:E24542-E24542(2011).
RN [17]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH RCF3 AND
RP CPL1, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=24146632; DOI=10.1371/journal.pgen.1003875;
RA Chen T., Cui P., Chen H., Ali S., Zhang S., Xiong L.;
RT "A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like
RT 1 and splicing factors and is important for pre-mRNA splicing in
RT Arabidopsis.";
RL PLoS Genet. 9:E1003875-E1003875(2013).
RN [18]
RP FUNCTION, AND INTERACTION WITH DRB1/HYL1 AND SE.
RX PubMed=26227967; DOI=10.1093/nar/gkv751;
RA Chen T., Cui P., Xiong L.;
RT "The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and
RT RS41 participate in miRNA biogenesis in Arabidopsis.";
RL Nucleic Acids Res. 43:8283-8298(2015).
CC -!- FUNCTION: Required for constitutive and alternative pre-mRNA splicing
CC (Probable). Involved in primary miRNA processing and pri-miRNA
CC biogenesis. Binds both intronless and intron-containing pri-miRNAs
CC (PubMed:26227967). {ECO:0000269|PubMed:26227967,
CC ECO:0000305|PubMed:24146632}.
CC -!- SUBUNIT: Component of the spliceosome (Probable). Interacts with
CC SNRNP35 (PubMed:15987817). Interacts with CYP59 (PubMed:16497658).
CC Interacts with RCF3 and CPL1 (PubMed:24146632). Interacts with
CC DRB1/HYL1 and SE (PubMed:26227967). {ECO:0000269|PubMed:15987817,
CC ECO:0000269|PubMed:16497658, ECO:0000269|PubMed:24146632,
CC ECO:0000269|PubMed:26227967, ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:24146632,
CC ECO:0000269|PubMed:26227967}. Nucleus speckle
CC {ECO:0000269|PubMed:15133128, ECO:0000269|PubMed:19245862,
CC ECO:0000269|PubMed:24146632, ECO:0000269|PubMed:26227967}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=P92965-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P92965-2; Sequence=VSP_054980;
CC Name=3;
CC IsoId=P92965-3; Sequence=VSP_054979;
CC -!- TISSUE SPECIFICITY: Highly expressed in roots and flowers. A presumably
CC longer alternatively spliced form is found in leaves, stems and
CC flowers. {ECO:0000269|PubMed:16936312}.
CC -!- DISRUPTION PHENOTYPE: Mutant seedlings show increased sensitivity to
CC salt stress and abscisic acid (ABA). {ECO:0000269|PubMed:24146632}.
CC -!- MISCELLANEOUS: The splicing pattern of the pre-mRNA is regulated in a
CC tissue-specific manner and by development, and changes in response to
CC various types of abiotic stresses. {ECO:0000305|PubMed:17319848}.
CC -!- SIMILARITY: Belongs to the splicing factor SR family. RS subfamily.
CC {ECO:0000305}.
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DR EMBL; X99437; CAA67800.1; -; mRNA.
DR EMBL; U76607; AAB18813.1; -; mRNA.
DR EMBL; AL022197; CAA18176.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85067.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85069.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85070.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66707.1; -; Genomic_DNA.
DR EMBL; AK317023; BAH19717.1; -; mRNA.
DR EMBL; AK317405; BAH20075.1; -; mRNA.
DR PIR; T05797; T05797.
DR RefSeq; NP_001078447.1; NM_001084978.3. [P92965-2]
DR RefSeq; NP_001190837.1; NM_001203908.1. [P92965-1]
DR RefSeq; NP_001328587.1; NM_001341747.1. [P92965-2]
DR RefSeq; NP_194280.1; NM_118682.4. [P92965-1]
DR AlphaFoldDB; P92965; -.
DR SMR; P92965; -.
DR BioGRID; 13941; 16.
DR IntAct; P92965; 2.
DR STRING; 3702.AT4G25500.4; -.
DR iPTMnet; P92965; -.
DR PaxDb; P92965; -.
DR PRIDE; P92965; -.
DR ProteomicsDB; 226570; -. [P92965-1]
DR EnsemblPlants; AT4G25500.1; AT4G25500.1; AT4G25500. [P92965-1]
DR EnsemblPlants; AT4G25500.3; AT4G25500.3; AT4G25500. [P92965-2]
DR EnsemblPlants; AT4G25500.4; AT4G25500.4; AT4G25500. [P92965-1]
DR EnsemblPlants; AT4G25500.6; AT4G25500.6; AT4G25500. [P92965-2]
DR GeneID; 828654; -.
DR Gramene; AT4G25500.1; AT4G25500.1; AT4G25500. [P92965-1]
DR Gramene; AT4G25500.3; AT4G25500.3; AT4G25500. [P92965-2]
DR Gramene; AT4G25500.4; AT4G25500.4; AT4G25500. [P92965-1]
DR Gramene; AT4G25500.6; AT4G25500.6; AT4G25500. [P92965-2]
DR KEGG; ath:AT4G25500; -.
DR Araport; AT4G25500; -.
DR TAIR; locus:2131864; AT4G25500.
DR eggNOG; KOG0106; Eukaryota.
DR HOGENOM; CLU_043462_3_0_1; -.
DR InParanoid; P92965; -.
DR OMA; IEWTKHE; -.
DR OrthoDB; 1563362at2759; -.
DR PhylomeDB; P92965; -.
DR PRO; PR:P92965; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; P92965; baseline and differential.
DR Genevisible; P92965; AT.
DR GO; GO:0010445; C:nuclear dicing body; IDA:TAIR.
DR GO; GO:0016607; C:nuclear speck; IDA:TAIR.
DR GO; GO:0005681; C:spliceosomal complex; ISS:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; ISS:TAIR.
DR GO; GO:0031053; P:primary miRNA processing; IGI:TAIR.
DR GO; GO:0008380; P:RNA splicing; NAS:TAIR.
DR Gene3D; 3.30.70.330; -; 2.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR Pfam; PF00076; RRM_1; 2.
DR SMART; SM00360; RRM; 2.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; mRNA processing; mRNA splicing; Nucleus;
KW Phosphoprotein; Reference proteome; Repeat; RNA-binding; Spliceosome.
FT CHAIN 1..350
FT /note="Serine/arginine-rich splicing factor RS40"
FT /id="PRO_0000081878"
FT DOMAIN 2..74
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 97..168
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 73..94
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 167..350
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 167..205
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 239..310
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 193
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P92964"
FT MOD_RES 195
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P92964"
FT MOD_RES 211
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 241
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P92964"
FT MOD_RES 262
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 278
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9SJA6"
FT MOD_RES 298
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
FT MOD_RES 308
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9FYB7"
FT MOD_RES 335
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P92966"
FT MOD_RES 340
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P92966"
FT VAR_SEQ 1..41
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_054979"
FT VAR_SEQ 1..35
FT /note="MKPVFCGNFEYDAREGDLERLFRKYGKVERVDMKA -> MQ (in
FT isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_054980"
FT CONFLICT 27
FT /note="K -> R (in Ref. 3; AAB18813)"
FT /evidence="ECO:0000305"
FT CONFLICT 63
FT /note="K -> R (in Ref. 3; AAB18813)"
FT /evidence="ECO:0000305"
FT CONFLICT 66
FT /note="R -> T (in Ref. 3; AAB18813)"
FT /evidence="ECO:0000305"
FT CONFLICT 139
FT /note="E -> K (in Ref. 8; BAH20075)"
FT /evidence="ECO:0000305"
FT CONFLICT 195
FT /note="S -> T (in Ref. 3; AAB18813)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 350 AA; 40319 MW; 4A1C779BB94B32A6 CRC64;
MKPVFCGNFE YDAREGDLER LFRKYGKVER VDMKAGFAFV YMEDERDAED AIRALDRFEF
GRKGRRLRVE WTKSERGGDK RSGGGSRRSS SSMRPSKTLF VINFDADNTR TRDLEKHFEP
YGKIVNVRIR RNFAFIQYEA QEDATRALDA SNNSKLMDKV ISVEYAVKDD DARGNGHSPE
RRRDRSPERR RRSPSPYKRE RGSPDYGRGA SPVAAYRKER TSPDYGRRRS PSPYKKSRRG
SPEYGRDRRG NDSPRRRERV ASPTKYSRSP NNKRERMSPN HSPFKKESPR NGVGEVESPI
ERRERSRSSP ENGQVESPGS IGRRDSDGGY DGAESPMQKS RSPRSPPADE
