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    PRP40 Prp40p [ Saccharomyces cerevisiae S288C ]

    Gene ID: 853857, updated on 4-Feb-2024

    Summary

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    Gene symbol
    PRP40
    Gene description
    Prp40p
    Primary source
    SGD:S000001495
    Locus tag
    YKL012W
    See related
    AllianceGenome:SGD:S000001495
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Saccharomyces cerevisiae S288C (strain: S288C)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
    Summary
    Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleus. Part of U1 snRNP and U2-type prespliceosome. Orthologous to human PRPF40A (pre-mRNA processing factor 40 homolog A) and PRPF40B (pre-mRNA processing factor 40 homolog B). [provided by Alliance of Genome Resources, Apr 2022]
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    Genomic context

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    Location:
    chromosome: XI
    Exon count:
    1
    Sequence:
    Chromosome: XI; NC_001143.9 (418310..420061)

    Chromosome XI - NC_001143.9Genomic Context describing neighboring genes Neighboring gene Urb1p Neighboring gene Arc19p Neighboring gene cruciform cutting endonuclease Neighboring gene putative ubiquitin-protein ligase UFD4

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001143.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Prp40 and early events in splice site definition. Becerra S, et al. Wiley Interdiscip Rev RNA, 2016 Jan-Feb. PMID 26494226
    2. Solution structure of the fourth FF domain of yeast Prp40 splicing factor. Bonet R, et al. Proteins, 2009 Dec. PMID 19722265
    3. Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle. Kao HY, et al. Mol Cell Biol, 1996 Mar. PMID 8622699, Free PMC Article
    4. The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains. Gasch A, et al. J Biol Chem, 2006 Jan 6. PMID 16253993
    5. WWP, a new amino acid motif present in single or multiple copies in various proteins including dystrophin and the SH3-binding Yes-associated protein YAP65. André B, et al. Biochem Biophys Res Commun, 1994 Dec 15. PMID 7802651

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Prp40 and early events in splice site definition
      Title: Prp40 and early events in splice site definition.
    2. Cloned and produced constructs corresponding to the FF2, FF3, and FF4 domains. Of these, only the constructs corresponding to FF4 gave a folded and stable sample.
      Title: Solution structure of the fourth FF domain of yeast Prp40 splicing factor.
    3. The C-terminal 2 FF domains of Prp40 are dispensable; deletion of additional FF domains is lethal; The first FF domain of Prp40 binds to U1 protein Luc7 and domains 2 and 3 bind to Snu71, another known U1 protein.
      Title: The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71.
    4. at least two different interaction surfaces exist in FF domains that have evolved to recognize distinct binding motifs
      Title: The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by SGD

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA cis splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U1 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U1 snRNP IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type prespliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type prespliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Prp40p
    NP_012913.3
    • U1 snRNP protein involved in splicing; interacts with the branchpoint-binding protein during the formation of the second commitment complex

    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_001143.9 Reference assembly

      Range
      418310..420061
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001179578.3 → NP_012913.3  TPA: Prp40p [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_012913.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VXS4, P33203
      UniProtKB/TrEMBL
      A0A8H4BYA2, A6ZZV3, C7GRH1, G2WI19, N1P7Z4
      Conserved Domains (1) summary
      COG5104
      Location:1 → 583
      PRP40; Splicing factor [RNA processing and modification]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    6N7P_J.1
    P33203.1

    Gene LinkOut

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