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Protein

Serine/arginine-rich splicing factor SR30

Gene

SR30

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Regulatory splicing factor that modulates alternative splicing and gene expression in specific cell types. Autoregulates its own expression. Probably involved in intron recognition and spliceosome assembly.1 Publication

GO - Molecular functioni

  1. mRNA binding Source: TAIR
  2. nucleotide binding Source: InterPro

GO - Biological processi

  1. mRNA splice site selection Source: TAIR
  2. regulation of mRNA splicing, via spliceosome Source: TAIR
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_180054. mRNA Splicing - Major Pathway.
REACT_236006. mRNA Splicing - Minor Pathway.
REACT_254005. mRNA 3'-end processing.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/arginine-rich splicing factor SR30
Short name:
At-SR30
Short name:
At-SRp30
Short name:
AtSR30
Alternative name(s):
SF2/ASF-like splicing modulator Srp30
Serine-arginine rich RNA binding protein 30
Gene namesi
Name:SR30
Synonyms:SRP30
Ordered Locus Names:At1g09140
ORF Names:T12M4.19
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 1

Organism-specific databases

TAIRiAT1G09140.

Subcellular locationi

Nucleus speckle. Nucleusnucleoplasm. Cytoplasm
Note: Inhibition of phosphorylation causes suppression of nuclear localization.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. interchromatin granule Source: TAIR
  3. nuclear speck Source: TAIR
  4. spliceosomal complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 268268Serine/arginine-rich splicing factor SR30PRO_0000429595Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei193 – 1931PhosphoserineBy similarity
Modified residuei210 – 2101PhosphoserineBy similarity
Modified residuei219 – 2191PhosphoserineBy similarity
Modified residuei221 – 2211PhosphoserineBy similarity
Modified residuei227 – 2271PhosphoserineBy similarity
Modified residuei236 – 2361PhosphoserineBy similarity
Modified residuei246 – 2461PhosphoserineBy similarity
Modified residuei256 – 2561PhosphoserineBy similarity
Modified residuei260 – 2601PhosphoserineBy similarity

Post-translational modificationi

Phosphorylated.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiQ949S8.

Expressioni

Tissue specificityi

Ubiquitous.2 Publications

Inductioni

Up-regulated by paraquat, high salt and early after high-light irradiation. Down-regulated by cold.3 Publications

Gene expression databases

ExpressionAtlasiQ9XFR5. baseline and differential.
GenevestigatoriQ9XFR5.

Interactioni

Subunit structurei

Component of the spliceosome. Interacts with SNRNP35, CYP59 and CYP63.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CYP63Q9LY754EBI-1540237,EBI-2360522

Protein-protein interaction databases

IntActiQ9XFR5. 13 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ9XFR5.
SMRiQ9XFR5. Positions 9-183.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 8276RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini109 – 18779RRM 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi181 – 26787Arg/Ser-rich (RS domain)Add
BLAST

Sequence similaritiesi

Belongs to the splicing factor SR family. SR subfamily.Curated
Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

HOGENOMiHOG000276234.
InParanoidiQ9XFR5.
KOiK12890.
OMAiRSHESRS.
PhylomeDBiQ9XFR5.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9XFR5-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSSRWNRTIY VGNLPGDIRK CEVEDLFYKY GPIVDIDLKI PPRPPGYAFV
60 70 80 90 100
EFEDPRDADD AIYGRDGYDF DGCRLRVEIA HGGRRFSPSV DRYSSSYSAS
110 120 130 140 150
RAPSRRSDYR VLVTGLPPSA SWQDLKDHMR KAGDVCFSEV FPDRKGMSGV
160 170 180 190 200
VDYSNYDDMK YAIRKLDATE FRNAFSSAYI RVREYESRSV SRSPDDSKSY
210 220 230 240 250
RSRSRSRGPS CSYSSKSRSV SPARSISPRS RPLSRSRSLY SSVSRSQSRS
260
KSRSRSRSNS PVSPVISG
Length:268
Mass (Da):30,386
Last modified:November 1, 1999 - v1
Checksum:i73BDC3534A8F9AC4
GO
Isoform 2 (identifier: Q9XFR5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     247-256: QSRSKSRSRS → GSLLRAGDWI
     257-268: Missing.

Note: No experimental confirmation available.

Show »
Length:256
Mass (Da):29,113
Checksum:i834FE60E6E8FC25E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti110 – 1101R → H in AAK93589 (PubMed:14593172).Curated
Sequence conflicti254 – 2541S → T in AAK93589 (PubMed:14593172).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei247 – 25610QSRSKSRSRS → GSLLRAGDWI in isoform 2. 1 PublicationVSP_054988
Alternative sequencei257 – 26812Missing in isoform 2. 1 PublicationVSP_054989Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131214 Genomic DNA. Translation: CAB42557.1.
AJ131214 Genomic DNA. Translation: CAB42558.1.
AC003114 Genomic DNA. No translation available.
CP002684 Genomic DNA. Translation: AEE28400.1.
CP002684 Genomic DNA. Translation: AEE28401.1.
AY150486 mRNA. Translation: AAN13011.1.
AY050912 mRNA. Translation: AAK93589.2.
RefSeqiNP_172386.3. NM_100783.5. [Q9XFR5-1]
NP_683288.2. NM_148447.3. [Q9XFR5-2]
UniGeneiAt.419.

Genome annotation databases

EnsemblPlantsiAT1G09140.1; AT1G09140.1; AT1G09140. [Q9XFR5-1]
AT1G09140.2; AT1G09140.2; AT1G09140. [Q9XFR5-2]
GeneIDi837433.
KEGGiath:AT1G09140.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131214 Genomic DNA. Translation: CAB42557.1.
AJ131214 Genomic DNA. Translation: CAB42558.1.
AC003114 Genomic DNA. No translation available.
CP002684 Genomic DNA. Translation: AEE28400.1.
CP002684 Genomic DNA. Translation: AEE28401.1.
AY150486 mRNA. Translation: AAN13011.1.
AY050912 mRNA. Translation: AAK93589.2.
RefSeqiNP_172386.3. NM_100783.5. [Q9XFR5-1]
NP_683288.2. NM_148447.3. [Q9XFR5-2]
UniGeneiAt.419.

3D structure databases

ProteinModelPortaliQ9XFR5.
SMRiQ9XFR5. Positions 9-183.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9XFR5. 13 interactions.

Proteomic databases

PRIDEiQ949S8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G09140.1; AT1G09140.1; AT1G09140. [Q9XFR5-1]
AT1G09140.2; AT1G09140.2; AT1G09140. [Q9XFR5-2]
GeneIDi837433.
KEGGiath:AT1G09140.

Organism-specific databases

TAIRiAT1G09140.

Phylogenomic databases

HOGENOMiHOG000276234.
InParanoidiQ9XFR5.
KOiK12890.
OMAiRSHESRS.
PhylomeDBiQ9XFR5.

Enzyme and pathway databases

ReactomeiREACT_180054. mRNA Splicing - Major Pathway.
REACT_236006. mRNA Splicing - Minor Pathway.
REACT_254005. mRNA 3'-end processing.

Gene expression databases

ExpressionAtlasiQ9XFR5. baseline and differential.
GenevestigatoriQ9XFR5.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes."
    Lopato S., Kalyna M., Dorner S., Kobayashi R., Krainer A.R., Barta A.
    Genes Dev. 13:987-1001(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 1 AND 2), FUNCTION, ALTERNATIVE SPLICING, TISSUE SPECIFICITY, PHOSPHORYLATION.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  5. "Interactions of Arabidopsis RS domain containing cyclophilins with SR proteins and U1 and U11 small nuclear ribonucleoprotein-specific proteins suggest their involvement in pre-mRNA Splicing."
    Lorkovic Z.J., Lopato S., Pexa M., Lehner R., Barta A.
    J. Biol. Chem. 279:33890-33898(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CYP63.
  6. "Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis."
    Fang Y., Hearn S., Spector D.L.
    Mol. Biol. Cell 15:2664-2673(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  7. "Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells."
    Lorkovic Z.J., Hilscher J., Barta A.
    Mol. Biol. Cell 15:3233-3243(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  8. "Evolutionary conservation of minor U12-type spliceosome between plants and humans."
    Lorkovic Z.J., Lehner R., Forstner C., Barta A.
    RNA 11:1095-1107(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SNRNP35.
  9. "AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II."
    Gullerova M., Barta A., Lorkovic Z.J.
    RNA 12:631-643(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CYP59.
  10. "Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress."
    Tanabe N., Yoshimura K., Kimura A., Yabuta Y., Shigeoka S.
    Plant Cell Physiol. 48:1036-1049(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE SPLICING, INDUCTION BY HIGH-LIGHT; PARAQUAT; COLD AND SALT STRESS.
  11. "Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses."
    Palusa S.G., Ali G.S., Reddy A.S.
    Plant J. 49:1091-1107(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE SPLICING, INDUCTION.
  12. "Plant SMU-1 and SMU-2 homologues regulate pre-mRNA splicing and multiple aspects of development."
    Chung T., Wang D., Kim C.S., Yadegari R., Larkins B.A.
    Plant Physiol. 151:1498-1512(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE SPLICING.
  13. "Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants."
    Barta A., Kalyna M., Reddy A.S.
    Plant Cell 22:2926-2929(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  14. "Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing."
    Richardson D.N., Rogers M.F., Labadorf A., Ben-Hur A., Guo H., Paterson A.H., Reddy A.S.N.
    PLoS ONE 6:E24542-E24542(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.
  15. "Subcellular and subnuclear distribution of high-light responsive serine/arginine-rich proteins, atSR45a and atSR30, in Arabidopsis thaliana."
    Mori T., Yoshimura K., Nosaka R., Sakuyama H., Koike Y., Tanabe N., Maruta T., Tamoi M., Shigeoka S.
    Biosci. Biotechnol. Biochem. 76:2075-2081(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION.
  16. Cited for: INDUCTION.

Entry informationi

Entry nameiSR30_ARATH
AccessioniPrimary (citable) accession number: Q9XFR5
Secondary accession number(s): Q949S8, Q9XFR6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: November 1, 1999
Last modified: March 4, 2015
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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 stress treatment (PubMed:10215626, PubMed:17556373, PubMed:17319848) or light regimes (PubMed:24763593).4 Publications
A mobile signal generated in the leaves triggers root alternative splicing responses to light.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.