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Q9XFR5

- SR30_ARATH

UniProt

Q9XFR5 - SR30_ARATH

Protein

Serine/arginine-rich splicing factor SR30

Gene

SR30

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 116 (01 Oct 2014)
      Sequence version 1 (01 Nov 1999)
      Previous versions | rss
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    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
    3. protein binding Source: IntAct

    GO - Biological processi

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

    Keywords - Biological processi

    mRNA processing, mRNA splicing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_180054. mRNA Splicing - Major Pathway.

    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

    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

    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

    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.
    OMAiSQVFRER.
    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. Align

    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

    MSSRWNRTIY VGNLPGDIRK CEVEDLFYKY GPIVDIDLKI PPRPPGYAFV    50
    EFEDPRDADD AIYGRDGYDF DGCRLRVEIA HGGRRFSPSV DRYSSSYSAS 100
    RAPSRRSDYR VLVTGLPPSA SWQDLKDHMR KAGDVCFSEV FPDRKGMSGV 150
    VDYSNYDDMK YAIRKLDATE FRNAFSSAYI RVREYESRSV SRSPDDSKSY 200
    RSRSRSRGPS CSYSSKSRSV SPARSISPRS RPLSRSRSLY SSVSRSQSRS 250
    KSRSRSRSNS PVSPVISG 268
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    RefSeqiNP_172386.3. NM_100783.5.
    NP_683288.2. NM_148447.3.
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    RefSeqi NP_172386.3. NM_100783.5.
    NP_683288.2. NM_148447.3.
    UniGenei At.419.

    3D structure databases

    ProteinModelPortali Q9XFR5.
    SMRi Q9XFR5. Positions 9-183.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q9XFR5. 13 interactions.

    Proteomic databases

    PRIDEi Q949S8.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G09140.1 ; AT1G09140.1 ; AT1G09140 . [Q9XFR5-1 ]
    AT1G09140.2 ; AT1G09140.2 ; AT1G09140 . [Q9XFR5-2 ]
    GeneIDi 837433.
    KEGGi ath:AT1G09140.

    Organism-specific databases

    TAIRi AT1G09140.

    Phylogenomic databases

    HOGENOMi HOG000276234.
    InParanoidi Q9XFR5.
    KOi K12890.
    OMAi SQVFRER.
    PhylomeDBi Q9XFR5.

    Enzyme and pathway databases

    Reactomei REACT_180054. mRNA Splicing - Major Pathway.

    Gene expression databases

    Genevestigatori Q9XFR5.

    Family and domain databases

    Gene3Di 3.30.70.330. 2 hits.
    InterProi IPR012677. Nucleotide-bd_a/b_plait.
    IPR000504. RRM_dom.
    [Graphical view ]
    Pfami PF00076. RRM_1. 2 hits.
    [Graphical view ]
    SMARTi SM00360. RRM. 2 hits.
    [Graphical view ]
    PROSITEi PS50102. RRM. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 116 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