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    FPA RNA binding protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 818942, updated on 18-Sep-2024

    Summary

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    Official Symbol
    FPA
    Official Full Name
    RNA binding protein
    Primary source
    TAIR:AT2G43410
    Locus tag
    AT2G43410
    See related
    Araport:AT2G43410
    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
    T1O24.15
    Summary
    FPA is a gene that regulates flowering time in Arabidopsis via a pathway that is independent of daylength (the autonomous pathway). Mutations in FPA result in extremely delayed flowering. Double mutants with FCA have reduced fertility and single/double mutants have defects in siRNA mediated chromatin silencing.
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    Genomic context

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    See FPA in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    8
    Sequence:
    Chromosome: 2; NC_003071.7 (18025247..18031255, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene electron-transfer flavoprotein:ubiquinone oxidoreductase Neighboring gene ncRNA Neighboring gene 3-beta hydroxysteroid dehydrogenase/isomerase family protein Neighboring gene glyoxalase 2-1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. Parker MT, et al. Elife, 2021 Apr 27. PMID 33904405, Free PMC Article
    2. Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA. Zhang Y, et al. PLoS One, 2016. PMID 27513867, Free PMC Article
    3. Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. Duc C, et al. PLoS Genet, 2013 Oct. PMID 24204292, Free PMC Article
    4. The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Hornyik C, et al. Dev Cell, 2010 Feb 16. PMID 20079695
    5. FPA, a gene involved in floral induction in Arabidopsis, encodes a protein containing RNA-recognition motifs. Schomburg FM, et al. Plant Cell, 2001 Jun. PMID 11402170, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA.
      Title: Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA.
    2. Fpa is a genetic suppressor of Ibm2.A complex regulation by IBM2 and FPA pathways in processing mRNAs of genes bearing heterochromatic marks.
      Title: Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin.
    3. The crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 A resolution is presented.
      Title: Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA.
    4. The recovery of the native ZOU gene expression in the spz2 zou-4 double mutant is caused by transcriptional read-through of the intronic T-DNA as a result of decreased proximal polyadenylation.
      Title: Reduced function of the RNA-binding protein FPA rescues a T-DNA insertion mutant in the Arabidopsis ZHOUPI gene by promoting transcriptional read-through.
    5. we show that defective termination at specific loci in fpa mutants is shared with dicer-like 1 (dcl1) or dcl4 mutants, leading us to develop alternative explanations for some silencing roles of these proteins
      Title: Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA.
    6. FCA and FPA play important roles in the A. thaliana genome in RNA 3' processing and transcription termination, thus limiting intergenic transcription.
      Title: RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription.
    7. FPA functions redundantly with FCA, another RNA binding protein that controls flowering and RNA silencing, to control the expression of alternatively polyadenylated antisense RNAs at the locus encoding the floral repressor FLC.
      Title: The spen family protein FPA controls alternative cleavage and polyadenylation of RNA.
    8. it is proposed that FCA and FPA regulate chromatin silencing of single and low-copy genes and interact in a locus-dependent manner with the canonical small interfering RNA-directed DNA methylation pathway to regulate common targets
      Title: Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing.
    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_001084577.2
    NM_001084578.1
    NM_001084579.2
    NM_001337027.1
    NM_001337028.1
    NM_129902.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within embryo development ending in seed dormancy IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo sac development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulatory ncRNA-mediated heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vegetative to reproductive phase transition of meristem IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    RNA binding protein
    NP_001078046.1
    • FPA; CONTAINS InterPro DOMAIN/s: Spen paralogue and orthologue SPOC, C-terminal (InterPro:IPR012921), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA recognition motif (RRM)-containing protein (TAIR:AT4G12640.1); Has 504799 Blast hits to 501692 proteins in 22138 species: Archae - 10949; Bacteria - 306025; Metazoa - 96089; Fungi - 13914; Plants - 29775; Viruses - 36050; Other Eukaryotes - 11997 (source: NCBI BLink).
    NP_001078047.1
    • FPA; CONTAINS InterPro DOMAIN/s: Spen paralogue and orthologue SPOC, C-terminal (InterPro:IPR012921), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA recognition motif (RRM)-containing protein (TAIR:AT4G12640.1); Has 504799 Blast hits to 501692 proteins in 22138 species: Archae - 10949; Bacteria - 306025; Metazoa - 96089; Fungi - 13914; Plants - 29775; Viruses - 36050; Other Eukaryotes - 11997 (source: NCBI BLink).
    NP_001078048.1
    • FPA; CONTAINS InterPro DOMAIN/s: Spen paralogue and orthologue SPOC, C-terminal (InterPro:IPR012921), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA recognition motif (RRM)-containing protein (TAIR:AT4G12640.1); Has 504799 Blast hits to 501692 proteins in 22138 species: Archae - 10949; Bacteria - 306025; Metazoa - 96089; Fungi - 13914; Plants - 29775; Viruses - 36050; Other Eukaryotes - 11997 (source: NCBI BLink).
    NP_181869.2
    • FPA; CONTAINS InterPro DOMAIN/s: Spen paralogue and orthologue SPOC, C-terminal (InterPro:IPR012921), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA recognition motif (RRM)-containing protein (TAIR:AT4G12640.1); Has 18609 Blast hits to 15572 proteins in 650 species: Archae - 12; Bacteria - 876; Metazoa - 10127; Fungi - 2512; Plants - 3298; Viruses - 9; Other Eukaryotes - 1775 (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_003071.7 Reference assembly

      Range
      18025247..18031255 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_129902.3 → NP_181869.2  RNA binding protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_181869.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A654F1J8
      Conserved Domains (3) summary
      cd12310
      Location:20 → 89
      RRM3_Spen; RNA recognition motif 3 in the Spen (split end) protein family
      pfam07744
      Location:398 → 494
      SPOC; SPOC domain
      pfam14179
      Location:718 → 787
      YppG; YppG-like protein

    2. NM_001084577.2 → NP_001078046.1  RNA binding protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078046.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8MQX1, B9DG59, C0Z2L9, O22855, Q58T22, Q8LPQ9
      UniProtKB/TrEMBL
      A0A654F1J8
      Conserved Domains (3) summary
      TIGR01628
      Location:19 → 383
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      pfam07744
      Location:434 → 560
      SPOC; SPOC domain
      cl17169
      Location:17 → 88
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_001084579.2 → NP_001078048.1  RNA binding protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078048.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8MQX1, B9DG59, C0Z2L9, O22855, Q58T22, Q8LPQ9
      UniProtKB/TrEMBL
      A0A654F1J8
      Conserved Domains (3) summary
      TIGR01628
      Location:19 → 383
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      pfam07744
      Location:434 → 560
      SPOC; SPOC domain
      cl17169
      Location:17 → 88
      RRM_SF; RNA recognition motif (RRM) superfamily

    4. NM_001084578.1 → NP_001078047.1  RNA binding protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078047.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A8MQX1, B9DG59, C0Z2L9, O22855, Q58T22, Q8LPQ9
      UniProtKB/TrEMBL
      A0A654F1J8
      Conserved Domains (3) summary
      TIGR01628
      Location:19 → 383
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      pfam07744
      Location:434 → 560
      SPOC; SPOC domain
      cl17169
      Location:17 → 88
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. NM_001337027.1 → NP_001323584.1  RNA binding protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VSZ7, A0A1P8AXG2, A0A654F1J8

    6. NM_001337028.1 → NP_001323585.1  RNA binding protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A654F1J8
      Conserved Domains (3) summary
      cd12310
      Location:20 → 89
      RRM3_Spen; RNA recognition motif 3 in the Spen (split end) protein family
      pfam07744
      Location:398 → 494
      SPOC; SPOC domain
      pfam14179
      Location:718 → 787
      YppG; YppG-like protein
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8LPQ9.2

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