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Serine/arginine-rich SC35-like splicing factor SCL30A (At-SCL30A) (AtSCL30A) (SC35-like splicing factor 30A) (Serine/arginine-rich splicing factor 30A)

 SL30A_ARATH             Reviewed;         262 AA.
Q9LHP2; Q9FYA8;
09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
02-JUN-2021, entry version 143.
RecName: Full=Serine/arginine-rich SC35-like splicing factor SCL30A;
Short=At-SCL30A;
Short=AtSCL30A;
AltName: Full=SC35-like splicing factor 30A;
AltName: Full=Serine/arginine-rich splicing factor 30A;
Name=SCL30A; OrderedLocusNames=At3g13570; ORFNames=K20M4.1;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA], AND INTERACTION WITH RS2Z33.
PubMed=12176998; DOI=10.1074/jbc.m206455200;
Lopato S., Forstner C., Kalyna M., Hilscher J., Langhammer U., Korakod L.,
Zdravko J., Barta A.;
"Network of interactions of a novel plant-specific Arg/Ser-rich protein,
atRSZ33, with atSC35-like splicing factors.";
J. Biol. Chem. 277:39989-39998(2002).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10907853; DOI=10.1093/dnares/7.3.217;
Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
clones.";
DNA Res. 7:217-221(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana reference
genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
SUBCELLULAR LOCATION.
PubMed=15133128; DOI=10.1091/mbc.e04-01-0055;
Lorkovic Z.J., Hilscher J., Barta A.;
"Use of fluorescent protein tags to study nuclear organization of the
spliceosomal machinery in transiently transformed living plant cells.";
Mol. Biol. Cell 15:3233-3243(2004).
[6]
INTERACTION WITH SNRNP35.
PubMed=15987817; DOI=10.1261/rna.2440305;
Lorkovic Z.J., Lehner R., Forstner C., Barta A.;
"Evolutionary conservation of minor U12-type spliceosome between plants and
humans.";
RNA 11:1095-1107(2005).
[7]
ALTERNATIVE SPLICING.
PubMed=16520337; DOI=10.1093/molbev/msj118;
Iida K., Go M.;
"Survey of conserved alternative splicing events of mRNAs encoding SR
proteins in land plants.";
Mol. Biol. Evol. 23:1085-1094(2006).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174; SER-176 AND SER-178, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=16807317; DOI=10.1093/nar/gkl429;
de la Fuente van Bentem S., Anrather D., Roitinger E., Djamei A.,
Hufnagl T., Barta A., Csaszar E., Dohnal I., Lecourieux D., Hirt H.;
"Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis
proteins involved in RNA metabolism.";
Nucleic Acids Res. 34:3267-3278(2006).
[9]
INTERACTION WITH CYP59.
PubMed=16497658; DOI=10.1261/rna.2226106;
Gullerova M., Barta A., Lorkovic Z.J.;
"AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that
interacts with SR proteins and the C-terminal domain of the RNA polymerase
II.";
RNA 12:631-643(2006).
[10]
ALTERNATIVE SPLICING, AND INDUCTION.
PubMed=17319848; DOI=10.1111/j.1365-313x.2006.03020.x;
Palusa S.G., Ali G.S., Reddy A.S.;
"Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich
proteins: regulation by hormones and stresses.";
Plant J. 49:1091-1107(2007).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-166, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19376835; DOI=10.1104/pp.109.138677;
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
Grossmann J., Gruissem W., Baginsky S.;
"Large-scale Arabidopsis phosphoproteome profiling reveals novel
chloroplast kinase substrates and phosphorylation networks.";
Plant Physiol. 150:889-903(2009).
[12]
GENE FAMILY, AND NOMENCLATURE.
PubMed=20884799; DOI=10.1105/tpc.110.078352;
Barta A., Kalyna M., Reddy A.S.;
"Implementing a rational and consistent nomenclature for serine/arginine-
rich protein splicing factors (SR proteins) in plants.";
Plant Cell 22:2926-2929(2010).
[13]
GENE FAMILY.
PubMed=21935421; DOI=10.1371/journal.pone.0024542;
Richardson D.N., Rogers M.F., Labadorf A., Ben-Hur A., Guo H.,
Paterson A.H., Reddy A.S.N.;
"Comparative analysis of serine/arginine-rich proteins across 27
eukaryotes: insights into sub-family classification and extent of
alternative splicing.";
PLoS ONE 6:E24542-E24542(2011).
[14]
FUNCTION, ALTERNATIVE SPLICING, AND DISRUPTION PHENOTYPE.
PubMed=22913769; DOI=10.1111/tpj.12004;
Thomas J., Palusa S.G., Prasad K.V., Ali G.S., Surabhi G.K., Ben-Hur A.,
Abdel-Ghany S.E., Reddy A.S.;
"Identification of an intronic splicing regulatory element involved in
auto-regulation of alternative splicing of SCL33 pre-mRNA.";
Plant J. 72:935-946(2012).
-!- FUNCTION: Involved in intron recognition and spliceosome assembly.
Binds probably to multiple 5'-GAAG-3' repeats found in its third
intron, suggesting autoregulation of alternative splicing
(PubMed:22913769). May be necessary for accurate splicing of the 3'
region of introns. {ECO:0000269|PubMed:22913769}.
-!- SUBUNIT: Component of the spliceosome. Interacts with SNRNP35, CYP59
and RS2Z33. {ECO:0000269|PubMed:12176998, ECO:0000269|PubMed:15987817,
ECO:0000269|PubMed:16497658}.
-!- INTERACTION:
Q9LHP2; Q1PDV2: SCL28; NbExp=2; IntAct=EBI-927082, EBI-927052;
Q9LHP2; Q8L3X8: SCL30; NbExp=3; IntAct=EBI-927082, EBI-927061;
-!- SUBCELLULAR LOCATION: Nucleus speckle {ECO:0000269|PubMed:15133128}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=A number of isoforms are produced. According to EST
sequences.;
Name=1;
IsoId=Q9LHP2-1; Sequence=Displayed;
-!- DISRUPTION PHENOTYPE: No effect on alternative splicing, due to the
redundancy with SCL33. Scl33 and scl30a double mutant shows altered
splicing. {ECO:0000269|PubMed:22913769}.
-!- MISCELLANEOUS: The splicing pattern of the pre-mRNA is regulated in a
tissue-specific manner and by development, and changes in response to
various types of abiotic stresses. {ECO:0000305|PubMed:17319848}.
-!- SIMILARITY: Belongs to the splicing factor SR family. SCL subfamily.
{ECO:0000305}.
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EMBL; AJ293800; CAC03604.1; -; mRNA.
EMBL; AP002038; BAB02599.1; -; Genomic_DNA.
EMBL; CP002686; AEE75375.1; -; Genomic_DNA.
EMBL; AF370268; AAK44083.1; -; mRNA.
EMBL; AY063026; AAL34200.1; -; mRNA.
RefSeq; NP_187966.1; NM_112203.4. [Q9LHP2-1]
SMR; Q9LHP2; -.
BioGRID; 5893; 12.
IntAct; Q9LHP2; 10.
STRING; 3702.AT3G13570.1; -.
iPTMnet; Q9LHP2; -.
PaxDb; Q9LHP2; -.
PRIDE; Q9LHP2; -.
ProteomicsDB; 232590; -. [Q9LHP2-1]
EnsemblPlants; AT3G13570.1; AT3G13570.1; AT3G13570. [Q9LHP2-1]
GeneID; 820559; -.
Gramene; AT3G13570.1; AT3G13570.1; AT3G13570. [Q9LHP2-1]
KEGG; ath:AT3G13570; -.
Araport; AT3G13570; -.
TAIR; locus:2086804; AT3G13570.
eggNOG; KOG0118; Eukaryota.
HOGENOM; CLU_012062_10_1_1; -.
InParanoid; Q9LHP2; -.
OMA; FHDQRDA; -.
OrthoDB; 1524134at2759; -.
PhylomeDB; Q9LHP2; -.
PRO; PR:Q9LHP2; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q9LHP2; baseline and differential.
Genevisible; Q9LHP2; AT.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0016607; C:nuclear speck; IDA:TAIR.
GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
GO; GO:0003729; F:mRNA binding; IDA:TAIR.
GO; GO:0003723; F:RNA binding; IBA:GO_Central.
GO; GO:0000398; P:mRNA splicing, via spliceosome; IGI:TAIR.
GO; GO:0008380; P:RNA splicing; NAS:TAIR.
Gene3D; 3.30.70.330; -; 1.
InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
InterPro; IPR035979; RBD_domain_sf.
InterPro; IPR000504; RRM_dom.
Pfam; PF00076; RRM_1; 1.
SMART; SM00360; RRM; 1.
SUPFAM; SSF54928; SSF54928; 1.
PROSITE; PS50102; RRM; 1.
1: Evidence at protein level;
Alternative splicing; mRNA processing; mRNA splicing; Nucleus;
Phosphoprotein; Reference proteome; RNA-binding; Spliceosome.
CHAIN 1..262
/note="Serine/arginine-rich SC35-like splicing factor
SCL30A"
/id="PRO_0000429601"
DOMAIN 37..115
/note="RRM"
/evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
REGION 1..38
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
REGION 115..262
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 115..144
/note="Basic and acidic residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 145..160
/note="Basic residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 175..193
/note="Basic and acidic residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 194..210
/note="Polar residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 222..262
/note="Polar residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
MOD_RES 9
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q8L3X8"
MOD_RES 20
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q8L3X8"
MOD_RES 166
/note="Phosphoserine"
/evidence="ECO:0007744|PubMed:19376835"
MOD_RES 174
/note="Phosphoserine"
/evidence="ECO:0007744|PubMed:16807317"
MOD_RES 176
/note="Phosphoserine"
/evidence="ECO:0007744|PubMed:16807317"
MOD_RES 178
/note="Phosphoserine"
/evidence="ECO:0007744|PubMed:16807317"
MOD_RES 191
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q8L3X8"
MOD_RES 193
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q8L3X8"
MOD_RES 235
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q8L3X8"
MOD_RES 259
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q9FMG4"
MOD_RES 261
/note="Phosphoserine"
/evidence="ECO:0000250|UniProtKB:Q9FMG4"
CONFLICT 149
/note="Missing (in Ref. 1; CAC03604)"
/evidence="ECO:0000305"
CONFLICT 162
/note="R -> C (in Ref. 1; CAC03604)"
/evidence="ECO:0000305"
SEQUENCE 262 AA; 30227 MW; A77DDEF4E9ECD7B2 CRC64;
MRGRSYTPSP PRGYGRRGRS PSPRGRFGGS RDSDLPTSLL VRNLRHDCRQ EDLRRPFEQF
GPVKDIYLPR DYYTGDPRGF GFIQFMDPAD AAEAKHQMDG YLLLGRELTV VFAEENRKKP
TEMRTRDRGG RSNRFQDRRR SPPRYSRSPP PRRGRRSRSR SRGYNSPPAK RHQSRSVSPQ
DRRYEKERSY SRSPPHNGSR VRSGSPGRVK SHSRSPRRSV SPRKNRSYTP EQARSQSPVP
RQSRSPTPVP RGAQNGDRSP SQ


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WP1983: Splicing factor NOVA regulated synpatic proteins
WP1046: Signaling of Hepatocyte Growth Factor Receptor
WP313: Signaling of Hepatocyte Growth Factor Receptor
WP1235: Signaling of Hepatocyte Growth Factor Receptor
WP927: Signaling of Hepatocyte Growth Factor Receptor
WP1899: Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs)
WP2148: Brain derived neurotrophic factor
WP1206: Signaling of Hepatocyte Growth Factor Receptor
WP444: Signaling of Hepatocyte Growth Factor Receptor
WP810: Signaling of Hepatocyte Growth Factor Receptor
WP1789: Binding of RNA by Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs)
WP272: Blood Clotting Cascade
WP1162: Signaling of Hepatocyte Growth Factor Receptor
WP94: Signaling of Hepatocyte Growth Factor Receptor
WP193: Signaling of Hepatocyte Growth Factor Receptor
WP2199: Seed Development
WP1642: D-Arginine and D-ornithine metabolism
WP459: Serine Biosynthesis
WP2185: Purine metabolism
WP275: Arginine Biosynthesis
WP1621: Arginine and proline metabolism
WP218: Serine and Glycine biosynthesis
WP390: Serine-isocitrate lyase pathway
WP142: mRNA processing
WP1659: Glycine, serine and threonine metabolism

Related Genes :
[SCL33 SR33 At1g55310 F7A10.15] Serine/arginine-rich SC35-like splicing factor SCL33 (At-SCL33) (AtSCL33) (SC35-like splicing factor 33) (Serine/arginine-rich splicing factor 33)
[SRSF2 SFRS2] Serine/arginine-rich splicing factor 2 (Protein PR264) (Splicing component, 35 kDa) (Splicing factor SC35) (SC-35) (Splicing factor, arginine/serine-rich 2)
[RS2Z33 RSZ33 At2g37340 F3G5.13] Serine/arginine-rich splicing factor RS2Z33 (RS-containing zinc finger protein 33) (At-RS2Z33) (At-RSZ33) (AtRSZ33)
[Srsf1 Sfrs1] Serine/arginine-rich splicing factor 1 (ASF/SF2) (Pre-mRNA-splicing factor SRp30a) (Splicing factor, arginine/serine-rich 1)
[SRSF1 ASF SF2 SF2P33 SFRS1 OK/SW-cl.3] Serine/arginine-rich splicing factor 1 (Alternative-splicing factor 1) (ASF-1) (Splicing factor, arginine/serine-rich 1) (pre-mRNA-splicing factor SF2, P33 subunit)
[SR45 RNPS1 At1g16610 F19K19.9] Serine/arginine-rich splicing factor SR45 (At-SR45) (AtSR45) (Serine/arginine-rich ribonucleoprotein 1)
[SR30 SRP30 At1g09140 T12M4.19] Serine/arginine-rich splicing factor SR30 (At-SR30) (At-SRp30) (AtSR30) (SF2/ASF-like splicing modulator Srp30) (Serine-arginine rich RNA binding protein 30)
[SRSF7 SFRS7] Serine/arginine-rich splicing factor 7 (Splicing factor 9G8) (Splicing factor, arginine/serine-rich 7)
[SRSF9 SFRS9 SRP30C] Serine/arginine-rich splicing factor 9 (Pre-mRNA-splicing factor SRp30C) (Splicing factor, arginine/serine-rich 9)
[RS31 RSP31 At3g61860 F21F14.30] Serine/arginine-rich splicing factor RS31 (At-RSp31) (AtRS31)
[SRSF2 SFRS2] Serine/arginine-rich splicing factor 2 (Splicing component, 35 kDa) (Splicing factor SC35) (SC-35) (Splicing factor, arginine/serine-rich 2)
[SR45A TRA2 At1g07350 F22G5.31] Serine/arginine-rich splicing factor SR45a (At-SR45A) (AtSR45a) (Protein TRANSFORMER2-like) (atTra2)
[SRSF2 SFRS2] Serine/arginine-rich splicing factor 2 (Splicing component, 35 kDa) (Splicing factor SC35) (SC-35) (Splicing factor, arginine/serine-rich 2)
[Srsf7 Sfrs7] Serine/arginine-rich splicing factor 7 (Splicing factor, arginine/serine-rich 7)
[Clasrp Clasp Sfrs16 Srsf16 Swap2] CLK4-associating serine/arginine rich protein (Clk4-associating SR-related protein) (Serine/arginine-rich splicing factor 16) (Splicing factor, arginine/serine-rich 16) (Suppressor of white-apricot homolog 2)
[TRA2B SFRS10] Transformer-2 protein homolog beta (TRA-2 beta) (TRA2-beta) (hTRA2-beta) (Splicing factor, arginine/serine-rich 10) (Transformer-2 protein homolog B)
[SRSF2 SFRS2] Serine/arginine-rich splicing factor 2 (Splicing component, 35 kDa) (Splicing factor SC35) (SC-35) (Splicing factor, arginine/serine-rich 2)
[Tra2b Sfrs10] Transformer-2 protein homolog beta (TRA-2 beta) (TRA2-beta) (RA301) (Splicing factor, arginine/serine-rich 10) (Transformer-2 protein homolog B)
[Tra2b Sfrs10 Silg41] Transformer-2 protein homolog beta (TRA-2 beta) (TRA2-beta) (Silica-induced gene 41 protein) (SIG-41) (Splicing factor, arginine/serine-rich 10) (Transformer-2 protein homolog B)
[CLASRP SFRS16 SWAP2 UNQ2428/PRO4988] CLK4-associating serine/arginine rich protein (Splicing factor, arginine/serine-rich 16) (Suppressor of white-apricot homolog 2)
[env] Envelope glycoprotein gp160 (Env polyprotein) [Cleaved into: Surface protein gp120 (SU) (Glycoprotein 120) (gp120); Transmembrane protein gp41 (TM) (Glycoprotein 41) (gp41)]
[unc-86 C30A5.7] Transcription factor unc-86 (Uncoordinated protein 86)
[rsp-2 srp-4 W02B12.2] Probable splicing factor, arginine/serine-rich 2 (CeSRp40) (RNA-binding protein srp-4)
[ARL6IP4] ADP-ribosylation factor-like protein 6-interacting protein 4 (ARL-6-interacting protein 4) (Aip-4) (HSP-975) (HSVI-binding protein) (SR-15) (SRp25) (SR-25) (Splicing factor SRrp37)
[Trim30a Rpt-1 Rpt1 Trim30] Tripartite motif-containing protein 30A (Down regulatory protein of interleukin-2 receptor) (Tripartite motif-containing protein 30)
[SRSF7 SFRS7] Serine/arginine-rich splicing factor 7 (Splicing factor, arginine/serine-rich 7)
[SRSF1 SFRS1] Serine/arginine-rich splicing factor 1 (Splicing factor, arginine/serine-rich 1)
[M] Matrix protein 2 (Proton channel protein M2)
[rsp-6 srp-1 C33H5.12] Probable splicing factor, arginine/serine-rich 6 (CeSRp20) (RNA-binding protein srp-1)
[SLC30A8 ZNT8] Zinc transporter 8 (ZnT-8) (Solute carrier family 30 member 8)

Bibliography :