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    Snrnp40 small nuclear ribonucleoprotein U5 subunit 40 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313056, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Snrnp40provided by RGD
    Official Full Name
    small nuclear ribonucleoprotein U5 subunit 40provided by RGD
    Primary source
    RGD:1309198
    See related
    Ensembl:ENSRNOG00000012219 AllianceGenome:RGD:1309198
    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
    Also known as
    RGD1309198
    Summary
    Predicted to be located in cytosol and nuclear speck. Predicted to be part of U2-type catalytic step 2 spliceosome. Orthologous to human SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 201.5), Spleen (RPKM 150.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    5q36
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (147984758..148017932)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (142700632..142733776)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (148577498..148610658)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 3 Neighboring gene zinc finger CCHC-type containing 17 Neighboring gene U6 spliceosomal RNA Neighboring gene ribosomal protein L10, pseudogene 6 Neighboring gene Sodium/potassium transporting ATPase interacting 1 Neighboring gene uncharacterized LOC134479033

    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. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Bertram K, et al. Nature, 2017 Feb 16. PMID 28076346
    2. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. Jurica MS, et al. RNA, 2002 Apr. PMID 11991638, Free PMC Article
    3. p38α MAPK proximity assay reveals a regulatory mechanism of alternative splicing in cardiomyocytes. Dumont AA, et al. Biochim Biophys Acta Mol Cell Res, 2019 Dec. PMID 31505169
    4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    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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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of U2-type catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    U5 small nuclear ribonucleoprotein 40 kDa protein
    Names
    small nuclear ribonucleoprotein 40 (U5)

    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_001134556.1 → NP_001128028.1  U5 small nuclear ribonucleoprotein 40 kDa protein

      See identical proteins and their annotated locations for NP_001128028.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473968
      UniProtKB/TrEMBL
      A6ISP1, D4A944
      Related
      ENSRNOP00000016325.6, ENSRNOT00000016325.8
      Conserved Domains (2) summary
      cd00200
      Location:63 → 352
      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:71 → 108
      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
      147984758..148017932
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063287574.1 → XP_063143644.1  U5 small nuclear ribonucleoprotein 40 kDa protein isoform X1

    2. XM_039109799.2 → XP_038965727.1  U5 small nuclear ribonucleoprotein 40 kDa protein isoform X2

      Conserved Domains (2) summary
      sd00039
      Location:21 → 56
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:2 → 176
      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 ...
    Nucleotide Protein Strain
    Heading Accession and Version

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