SRC28_ARATH
ID SRC28_ARATH Reviewed; 236 AA.
AC Q1PDV2; A0MFG8; Q8GTR7; Q9FYB0;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Serine/arginine-rich SC35-like splicing factor SCL28;
DE Short=At-SCL28;
DE Short=AtSCL28;
DE AltName: Full=28 kDa SC35-like splicing factor;
DE AltName: Full=SC35-like splicing factor 28;
DE AltName: Full=Serine/arginine-rich splicing factor 28;
GN Name=SCL28; OrderedLocusNames=At5g18810; ORFNames=F17K4.60;
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], AND INTERACTION WITH RS2Z33.
RX PubMed=12176998; DOI=10.1074/jbc.m206455200;
RA Lopato S., Forstner C., Kalyna M., Hilscher J., Langhammer U., Korakod L.,
RA Zdravko J., Barta A.;
RT "Network of interactions of a novel plant-specific Arg/Ser-rich protein,
RT atRSZ33, with atSC35-like splicing factors.";
RL J. Biol. Chem. 277:39989-39998(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=17147637; DOI=10.1111/j.1467-7652.2006.00183.x;
RA Underwood B.A., Vanderhaeghen R., Whitford R., Town C.D., Hilson P.;
RT "Simultaneous high-throughput recombinational cloning of open reading
RT frames in closed and open configurations.";
RL Plant Biotechnol. J. 4:317-324(2006).
RN [6]
RP INTERACTION WITH CYP63 AND CYP95.
RX PubMed=15166240; DOI=10.1074/jbc.m400270200;
RA Lorkovic Z.J., Lopato S., Pexa M., Lehner R., Barta A.;
RT "Interactions of Arabidopsis RS domain containing cyclophilins with SR
RT proteins and U1 and U11 small nuclear ribonucleoprotein-specific proteins
RT suggest their involvement in pre-mRNA Splicing.";
RL J. Biol. Chem. 279:33890-33898(2004).
RN [7]
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 [8]
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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-184, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [10]
RP 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 [11]
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 [12]
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).
CC -!- FUNCTION: Involved in intron recognition and spliceosome assembly
CC (Probable). Probably active at the 5' splice sites. {ECO:0000305}.
CC -!- SUBUNIT: Component of the spliceosome. Interacts with RS2Z33, CYP59,
CC CYP63 and CYP95. {ECO:0000269|PubMed:12176998,
CC ECO:0000269|PubMed:15166240, ECO:0000269|PubMed:16497658}.
CC -!- INTERACTION:
CC Q1PDV2; Q9LY75: CYP63; NbExp=4; IntAct=EBI-927052, EBI-2360522;
CC Q1PDV2; Q8L3X8: SCL30; NbExp=3; IntAct=EBI-927052, EBI-927061;
CC Q1PDV2; Q9LHP2: SCL30A; NbExp=2; IntAct=EBI-927052, EBI-927082;
CC -!- SUBCELLULAR LOCATION: Nucleus speckle {ECO:0000269|PubMed:15133128}.
CC -!- SIMILARITY: Belongs to the splicing factor SR family. SCL subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABK28702.1; Type=Erroneous termination; Note=Extended C-terminus.; Evidence={ECO:0000305};
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DR EMBL; AJ293797; CAC03601.1; -; mRNA.
DR EMBL; AC068655; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED92615.1; -; Genomic_DNA.
DR EMBL; AK118752; BAC43345.1; -; mRNA.
DR EMBL; DQ446966; ABE66166.1; -; mRNA.
DR EMBL; DQ653294; ABK28702.1; ALT_SEQ; mRNA.
DR RefSeq; NP_197382.3; NM_121886.4.
DR AlphaFoldDB; Q1PDV2; -.
DR SMR; Q1PDV2; -.
DR BioGRID; 17275; 13.
DR IntAct; Q1PDV2; 12.
DR STRING; 3702.AT5G18810.1; -.
DR iPTMnet; Q1PDV2; -.
DR PaxDb; Q1PDV2; -.
DR PRIDE; Q1PDV2; -.
DR ProteomicsDB; 226916; -.
DR EnsemblPlants; AT5G18810.1; AT5G18810.1; AT5G18810.
DR GeneID; 831999; -.
DR Gramene; AT5G18810.1; AT5G18810.1; AT5G18810.
DR KEGG; ath:AT5G18810; -.
DR Araport; AT5G18810; -.
DR TAIR; locus:2144945; AT5G18810.
DR eggNOG; KOG0118; Eukaryota.
DR HOGENOM; CLU_012062_10_1_1; -.
DR OMA; FHDQRDA; -.
DR OrthoDB; 1524134at2759; -.
DR PhylomeDB; Q1PDV2; -.
DR PRO; PR:Q1PDV2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q1PDV2; baseline and differential.
DR Genevisible; Q1PDV2; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0016607; C:nuclear speck; IDA:TAIR.
DR GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR Gene3D; 3.30.70.330; -; 1.
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; 1.
DR SMART; SM00360; RRM; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 1.
PE 1: Evidence at protein level;
KW mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding; Spliceosome.
FT CHAIN 1..236
FT /note="Serine/arginine-rich SC35-like splicing factor
FT SCL28"
FT /id="PRO_0000429599"
FT DOMAIN 47..125
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 124..219
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 10..41
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 148..171
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 172..219
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 184
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157"
FT CONFLICT 82..84
FT /note="YYT -> FNS (in Ref. 1; CAC03601)"
FT /evidence="ECO:0000305"
FT CONFLICT 130
FT /note="P -> T (in Ref. 4; BAC43345)"
FT /evidence="ECO:0000305"
FT CONFLICT 143
FT /note="H -> R (in Ref. 4; BAC43345)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 236 AA; 28028 MW; 1328AAD75AF1713B CRC64;
MARARSRSRS YSPRPRDRSP PRERKGYDDN RLRERPSSRD HESSGPSGLL IRNLPLDARP
NDLRDSFERF GPLKDIYLPR NYYTGEPRGF GFVKYRYAED AAEAMKRMNH KVIGGREIAI
VFAEENRKTP QEMRTTNGTS GRHGDYKRTS HRSPRRRYRS HSRSRSPPRR ESRHSKVRED
DLYSPRRRSR SISRSPLPRN EREYKSRNCR SPREERVLTP IRSRCLSRSR SRSLSR
