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

Gene ID: 298095, updated on 5-Mar-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
Ensembl: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 processing factor 4). [provided by Alliance of Genome Resources, Apr 2022]
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, ENSRNOT00000019910.6
    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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