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    Prpf4 pre-mRNA splicing tri-snRNP complex factor 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 298095, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Prpf4provided by RGD
    Official Full Name
    pre-mRNA splicing tri-snRNP complex factor 4provided by RGD
    Primary source
    RGD:1311303
    See related
    EnsemblRapid:ENSRNOG00000014777 AllianceGenome:RGD:1311303
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable U4 snRNA binding activity and U6 snRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in Cajal body and nuclear speck. Predicted to be part of U2-type precatalytic spliceosome; U4/U6 snRNP; and U4/U6 x U5 tri-snRNP complex. Human ortholog(s) of this gene implicated in retinitis pigmentosa 70. Orthologous to human PRPF4 (pre-mRNA splicing tri-snRNP complex factor PRPF4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 140.2), Thymus (RPKM 125.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prpf4 in Genome Data Viewer
    Location:
    5q24
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (80875511..80889501)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (75859934..75873924)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (78267248..78281172)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene FKBP prolyl isomerase family member 15 Neighboring gene solute carrier family 31 member 1 Neighboring gene cell division cycle 26 Neighboring gene ring finger protein 183 Neighboring gene WD repeat domain 31

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The 20kD protein of human [U4/U6.U5] tri-snRNPs is a novel cyclophilin that forms a complex with the U4/U6-specific 60kD and 90kD proteins. Teigelkamp S, et al. RNA, 1998 Feb. PMID 9570313, Free PMC Article
    2. Identification of a PRPF4 loss-of-function variant that abrogates U4/U6.U5 tri-snRNP integration and is associated with retinitis pigmentosa. Linder B, et al. PLoS One, 2014. PMID 25383878, Free PMC Article
    3. RNAi knockdown of hPrp31 leads to an accumulation of U4/U6 di-snRNPs in Cajal bodies. Schaffert N, et al. EMBO J, 2004 Aug 4. PMID 15257298, Free PMC Article
    4. The nuclear cap-binding complex interacts with the U4/U6·U5 tri-snRNP and promotes spliceosome assembly in mammalian cells. Pabis M, et al. RNA, 2013 Aug. PMID 23793891, Free PMC Article
    5. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    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 RGD

    Function Evidence Code Pubs
    enables U4 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables U6 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Cajal body ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type precatalytic spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U4/U6 snRNP ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of spliceosomal snRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    U4/U6 small nuclear ribonucleoprotein Prp4
    Names
    PRP4 pre-mRNA processing factor 4 homolog
    pre-mRNA processing factor 4

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001106659.1 → NP_001100129.1  U4/U6 small nuclear ribonucleoprotein Prp4

      See identical proteins and their annotated locations for NP_001100129.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473978
      UniProtKB/TrEMBL
      A6J7U4, D4A7J8
      Related
      ENSRNOP00000019910.4, ENSRNOT00000019910.7
      Conserved Domains (4) summary
      smart00500
      Location:102 → 140
      SFM; Splicing Factor Motif, present in Prp18 and Pr04
      COG2319
      Location:227 → 518
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:232 → 518
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00039
      Location:233 → 270
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      80875511..80889501
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109466.2 → XP_038965394.1  U4/U6 small nuclear ribonucleoprotein Prp4 isoform X1

      Conserved Domains (2) summary
      cd00200
      Location:8 → 276
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00039
      Location:42 → 78
      7WD40; WD40 repeat [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version

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