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    RS40 arginine/serine-rich splicing factor 35 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 828654, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RS40
    Official Full Name
    arginine/serine-rich splicing factor 35
    Primary source
    TAIR:AT4G25500
    Locus tag
    AT4G25500
    See related
    Araport:AT4G25500
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ARABIDOPSIS THALIANA ARGININE/SERINE-RICH SPLICING FACTOR 35; ARGININE/SERINE-RICH SPLICING FACTOR; arginine/serine-rich splicing factor 35; arginine/serine-rich splicing factor 40; At-RS40; AT-SRP40; ATRSP35; ATRSP40; RSP35; SPLICING FACTOR AT-SRP40; T30C3.9
    Summary
    encodes an arginine/serine-rich splicing factor. transcript is alternatively spliced and is differentially expressed in different tissues (flowers, roots, stems, and leaves) examined. Barta et al (2010) have proposed a nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR proteins): Plant Cell. 2010, 22:2926.
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    Genomic context

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    See RS40 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    8
    Sequence:
    Chromosome: 4; NC_003075.7 (13024498..13027484)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene miscRNA Neighboring gene C-repeat/DRE binding factor 1 Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene SEUSS-like 3

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis. Lopato S, et al. Plant Cell, 1996 Dec. PMID 8989882, Free PMC Article
    2. A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis. Chen T, et al. PLoS Genet, 2013. PMID 24146632, Free PMC Article
    3. The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Chen T, et al. Nucleic Acids Res, 2015 Sep 30. PMID 26227967, Free PMC Article
    4. 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, et al. RNA, 2006 Apr. PMID 16497658, Free PMC Article
    5. Evolutionary conservation of minor U12-type spliceosome between plants and humans. Lorkovic ZJ, et al. RNA, 2005 Jul. PMID 15987817, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Serine/arginine-rich splicing factors RS40 and RS41 affect the biogenesis of a subset of miRNA. [RS40]
      Title: The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001203908.1
    NM_001341745.1
    NM_001341746.1
    NM_001341747.1
    NM_001341748.1
    NM_118682.4
    NM_202887.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    acts_upstream_of_or_within primary miRNA processing IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear dicing body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    part_of spliceosomal complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    arginine/serine-rich splicing factor 35
    NP_001078447.1
    • arginine/serine-rich splicing factor 35 (RSP35); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: nuclear mRNA splicing, via spliceosome, RNA splicing; LOCATED IN: nuclear speck, spliceosomal complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA-binding (RRM/RBD/RNP motifs) family protein (TAIR:AT5G52040.4); Has 12133 Blast hits to 9335 proteins in 376 species: Archae - 0; Bacteria - 104; Metazoa - 8049; Fungi - 1339; Plants - 1578; Viruses - 48; Other Eukaryotes - 1015 (source: NCBI BLink).
    NP_001190837.1
    • arginine/serine-rich splicing factor 35 (RSP35); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: nuclear mRNA splicing, via spliceosome, RNA splicing; LOCATED IN: nuclear speck, spliceosomal complex; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA-binding (RRM/RBD/RNP motifs) family protein (TAIR:AT5G52040.2).
    NP_001320063.1
    • arginine/serine-rich splicing factor 35 (RSP35); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: nuclear mRNA splicing, via spliceosome, RNA splicing; LOCATED IN: nuclear speck, spliceosomal complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA-binding (RRM/RBD/RNP motifs) family protein (TAIR:AT5G52040.4); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_194280.1
    • arginine/serine-rich splicing factor 35 (RSP35); FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: nuclear mRNA splicing, via spliceosome, RNA splicing; LOCATED IN: nuclear speck, spliceosomal complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA-binding (RRM/RBD/RNP motifs) family protein (TAIR:AT5G52040.2); Has 15818 Blast hits to 12132 proteins in 578 species: Archae - 10; Bacteria - 734; Metazoa - 9656; Fungi - 1783; Plants - 2169; Viruses - 46; Other Eukaryotes - 1420 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003075.7 Reference assembly

      Range
      13024498..13027484
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001084978.3 → NP_001078447.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078447.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2F2E8
      Conserved Domains (1) summary
      cl17169
      Location:65 → 134
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_118682.4 → NP_194280.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_194280.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8MRZ9, B9DH58, F4JSN1, P92965, Q96333
      UniProtKB/TrEMBL
      A0A654FSN0, Q9M0K9
      Conserved Domains (2) summary
      cd12234
      Location:2 → 73
      RRM1_AtRSp31_like; RNA recognition motif (RRM) found in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants
      cl17169
      Location:98 → 167
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_001341746.1 → NP_001328585.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178V577, A0A1P8B539, A0A384KI10, A0A7G2F2E8
      Conserved Domains (1) summary
      cl17169
      Location:77 → 146
      RRM_SF; RNA recognition motif (RRM) superfamily

    4. NM_001341745.1 → NP_001320063.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178V577, A0A1P8B539, A0A384KI10, A0A7G2F2E8
      Conserved Domains (1) summary
      cl17169
      Location:77 → 146
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. NM_001341747.1 → NP_001328587.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2F2E8
      Conserved Domains (1) summary
      cl17169
      Location:65 → 134
      RRM_SF; RNA recognition motif (RRM) superfamily

    6. NM_001203908.1 → NP_001190837.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190837.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8MRZ9, B9DH58, F4JSN1, P92965, Q96333
      UniProtKB/TrEMBL
      A0A654FSN0, Q9M0K9
      Conserved Domains (2) summary
      cd12234
      Location:2 → 73
      RRM1_AtRSp31_like; RNA recognition motif (RRM) found in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants
      cl17169
      Location:98 → 167
      RRM_SF; RNA recognition motif (RRM) superfamily

    7. NM_001341748.1 → NP_001328586.1  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178V577, A0A1P8B539, A0A384KI10, A0A7G2F2E8
      Conserved Domains (1) summary
      cl17169
      Location:77 → 146
      RRM_SF; RNA recognition motif (RRM) superfamily

    8. NM_202887.3 → NP_974616.2  arginine/serine-rich splicing factor 35 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178V577, A0A1P8B539, A0A384KI10, A0A7G2F2E8
      Conserved Domains (1) summary
      cl17169
      Location:77 → 146
      RRM_SF; RNA recognition motif (RRM) superfamily
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P92965.2

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