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Q9XFR5 (SR30_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:SR30
Synonyms:SRP30
Ordered Locus Names:At1g09140
ORF Names:T12M4.19
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length268 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1

Subunit structure

Component of the spliceosome. Interacts with SNRNP35, CYP59 and CYP63. Ref.5 Ref.8 Ref.9

Subcellular location

Nucleus speckle. Nucleusnucleoplasm. Cytoplasm. Note: Inhibition of phosphorylation causes suppression of nuclear localization. Ref.6 Ref.7 Ref.15

Tissue specificity

Ubiquitous. Ref.1 Ref.6

Induction

Up-regulated by paraquat, high salt and early after high-light irradiation. Down-regulated by cold. Ref.10 Ref.11 Ref.16

Post-translational modification

Phosphorylated. Ref.1 Ref.15

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 (Ref.1, Ref.10, Ref.11) or light regimes (Ref.16).

A mobile signal generated in the leaves triggers root alternative splicing responses to light (Ref.16).

Sequence similarities

Belongs to the splicing factor SR family. SR subfamily.

Contains 2 RRM (RNA recognition motif) domains.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

MAA21_30Q9LY754EBI-1540237,EBI-2360522

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9XFR5-1)

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.
Isoform 2 (identifier: Q9XFR5-2)

The sequence of this isoform differs from the canonical sequence as follows:
     247-256: QSRSKSRSRS → GSLLRAGDWI
     257-268: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 268268Serine/arginine-rich splicing factor SR30
PRO_0000429595

Regions

Domain7 – 8276RRM 1
Domain109 – 18779RRM 2
Compositional bias181 – 26787Arg/Ser-rich (RS domain)

Natural variations

Alternative sequence247 – 25610QSRSKSRSRS → GSLLRAGDWI in isoform 2.
VSP_054988
Alternative sequence257 – 26812Missing in isoform 2.
VSP_054989

Experimental info

Sequence conflict1101R → H in AAK93589. Ref.4
Sequence conflict2541S → T in AAK93589. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 73BDC3534A8F9AC4

FASTA26830,386
        10         20         30         40         50         60 
MSSRWNRTIY VGNLPGDIRK CEVEDLFYKY GPIVDIDLKI PPRPPGYAFV EFEDPRDADD 

        70         80         90        100        110        120 
AIYGRDGYDF DGCRLRVEIA HGGRRFSPSV DRYSSSYSAS RAPSRRSDYR VLVTGLPPSA 

       130        140        150        160        170        180 
SWQDLKDHMR KAGDVCFSEV FPDRKGMSGV VDYSNYDDMK YAIRKLDATE FRNAFSSAYI 

       190        200        210        220        230        240 
RVREYESRSV SRSPDDSKSY RSRSRSRGPS CSYSSKSRSV SPARSISPRS RPLSRSRSLY 

       250        260 
SSVSRSQSRS KSRSRSRSNS PVSPVISG 

« Hide

Isoform 2 [UniParc].

Checksum: 834FE60E6E8FC25E
Show »

FASTA25629,113

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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]"A chloroplast retrograde signal regulates nuclear alternative splicing."
Petrillo E., Herz M.A., Fuchs A., Reifer D., Fuller J., Yanovsky M.J., Simpson C., Brown J.W., Barta A., Kalyna M., Kornblihtt A.R.
Science 344:427-430(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ131214 Genomic DNA. Translation: CAB42557.1.
AJ131214 Genomic DNA. Translation: CAB42558.1.
CP002684 Genomic DNA. Translation: AEE28400.1.
CP002684 Genomic DNA. Translation: AEE28401.1.
AY150486 mRNA. Translation: AAN13011.1.
AY050912 mRNA. Translation: AAK93589.2.
RefSeqNP_172386.3. NM_100783.5.
UniGeneAt.419.

3D structure databases

ProteinModelPortalQ9XFR5.
SMRQ9XFR5. Positions 9-183.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEQ949S8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G09140.1; AT1G09140.1; AT1G09140.
GeneID837433.
KEGGath:AT1G09140.

Organism-specific databases

TAIRAT1G09140.

Phylogenomic databases

HOGENOMHOG000276234.
InParanoidQ9XFR5.
KOK12890.
OMASQVFRER.
PhylomeDBQ9XFR5.

Gene expression databases

GenevestigatorQ9XFR5.

Family and domain databases

Gene3D3.30.70.330. 2 hits.
InterProIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTSM00360. RRM. 2 hits.
[Graphical view]
PROSITEPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameSR30_ARATH
AccessionPrimary (citable) accession number: Q9XFR5
Secondary accession number(s): Q949S8, Q9XFR6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: November 1, 1999
Last modified: July 9, 2014
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names