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    Pre-mRNA-splicing factor 3 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 839699, updated on 18-Sep-2024

    Summary

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    Official Full Name
    Pre-mRNA-splicing factor 3
    Primary source
    TAIR:AT1G28060
    Locus tag
    AT1G28060
    See related
    Araport:AT1G28060
    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
    F13K9.16; F13K9_16; RDM16; RNA-directed DNA methylation 16
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    Genomic context

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    Location:
    chromosome: 1
    Exon count:
    7
    Sequence:
    Chromosome: 1; NC_003070.9 (9778851..9782907)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene RING/U-box superfamily protein Neighboring gene B-box type zinc finger protein with CCT domain-containing protein Neighboring gene ATP-dependent RNA helicase Neighboring gene RING finger protein Neighboring gene ncRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. Huang CF, et al. PLoS Genet, 2013. PMID 24068953, Free PMC Article
    2. RDM16 and STA1 regulate differential usage of exon/intron in RNA directed DNA methylation pathway. Sharma RD, et al. Gene, 2017 Apr 20. PMID 28153750
    3. Regulation of plant immunity through ubiquitin-mediated modulation of Ca(2+) -calmodulin-AtSR1/CAMTA3 signaling. Zhang L, et al. Plant J, 2014 Apr. PMID 24528504
    4. A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. McWhite CD, et al. Cell, 2020 Apr 16. PMID 32191846, Free PMC Article
    5. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001332796.1
    NM_001332797.1
    NM_102571.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryo development ending in seed dormancy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_positive_effect gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U4/U6 x U5 tri-snRNP complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm 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
    Pre-mRNA-splicing factor 3
    NP_001319094.1
    • Pre-mRNA-splicing factor 3; CONTAINS InterPro DOMAIN/s: Pre-mRNA-splicing factor 3 (InterPro:IPR013881); BEST Arabidopsis thaliana protein match is: Pre-mRNA-splicing factor 3 (TAIR:AT3G55930.1); Has 22923 Blast hits to 12760 proteins in 707 species: Archae - 18; Bacteria - 1085; Metazoa - 11525; Fungi - 3053; Plants - 1999; Viruses - 93; Other Eukaryotes - 5150 (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_003070.9 Reference assembly

      Range
      9778851..9782907
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001332796.1 → NP_001319094.1  Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8H0S1, Q9C7E7
      UniProtKB/TrEMBL
      A0A178WNB3, A0A5S9W5H6
      Conserved Domains (3) summary
      TIGR01622
      Location:38 → 105
      SF-CC1; splicing factor, CC1-like family
      pfam06544
      Location:657 → 780
      DUF1115; Protein of unknown function (DUF1115)
      pfam08572
      Location:404 → 631
      PRP3; pre-mRNA processing factor 3 (PRP3)

    2. NM_102571.3 → NP_174127.1  Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_174127.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8H0S1, Q9C7E7
      UniProtKB/TrEMBL
      A0A178WNB3, A0A5S9W5H6
      Conserved Domains (3) summary
      TIGR01622
      Location:38 → 105
      SF-CC1; splicing factor, CC1-like family
      pfam06544
      Location:657 → 780
      DUF1115; Protein of unknown function (DUF1115)
      pfam08572
      Location:404 → 631
      PRP3; pre-mRNA processing factor 3 (PRP3)

    3. NM_001332797.1 → NP_001321377.1  Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8H0S1, Q9C7E7
      UniProtKB/TrEMBL
      A0A178WNB3, A0A5S9W5H6
      Conserved Domains (3) summary
      TIGR01622
      Location:38 → 105
      SF-CC1; splicing factor, CC1-like family
      pfam06544
      Location:657 → 780
      DUF1115; Protein of unknown function (DUF1115)
      pfam08572
      Location:404 → 631
      PRP3; pre-mRNA processing factor 3 (PRP3)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C7E7.1

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