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    Trub1 TruB pseudouridine synthase family member 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361775, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Trub1provided by RGD
    Official Full Name
    TruB pseudouridine synthase family member 1provided by RGD
    Primary source
    RGD:1308502
    See related
    EnsemblRapid:ENSRNOG00000017321 AllianceGenome:RGD:1308502
    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 pre-miRNA binding activity and pseudouridine synthase activity. Predicted to be involved in mRNA pseudouridine synthesis; positive regulation of pre-miRNA processing; and tRNA modification. Predicted to be located in cytosol and mitochondrion. Predicted to be active in nucleus. Orthologous to human TRUB1 (TruB pseudouridine synthase family member 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 43.7), Kidney (RPKM 30.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Trub1 in Genome Data Viewer
    Location:
    1q55
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (266518510..266559633)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (256513418..256554549)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (278311362..278418347)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485259 Neighboring gene microRNA 6316 Neighboring gene uncharacterized LOC102551125 Neighboring gene uncharacterized LOC134485260

    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. TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. Safra M, et al. Genome Res, 2017 Mar. PMID 28073919, Free PMC Article
    2. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Morgenstern M, et al. Cell Metab, 2021 Dec 7. PMID 34800366, Free PMC Article
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    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

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables pre-miRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables pre-miRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables pseudouridine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pseudouridine synthase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables pseudouridine synthase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables tRNA pseudouridine(55) synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA pseudouridine synthesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA pseudouridine synthesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of pre-miRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of pre-miRNA processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in tRNA modification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA modification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA modification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    pseudouridylate synthase TRUB1
    Names
    TruB pseudouridine (psi) synthase family member 1
    TruB pseudouridine (psi) synthase homolog 1
    probable tRNA pseudouridine synthase 1
    psi55 synthase TRUB1
    tRNA pseudouridine 55 synthase TRUB1
    truB pseudouridine synthase homolog 1
    NP_001012173.1
    XP_008758760.1
    XP_038940620.1
    XP_038940629.1
    XP_038940649.1
    XP_038940651.1

    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_001012173.1 → NP_001012173.1  pseudouridylate synthase TRUB1

      See identical proteins and their annotated locations for NP_001012173.1

      Status: PROVISIONAL

      Source sequence(s)
      BC087683
      UniProtKB/Swiss-Prot
      Q5M934
      UniProtKB/TrEMBL
      A6JI44
      Related
      ENSRNOP00000023309.2, ENSRNOT00000023309.6
      Conserved Domains (2) summary
      TIGR00431
      Location:61 → 278
      TruB; tRNA pseudouridine(55) synthase
      cl00130
      Location:61 → 336
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    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_086019.1 Reference GRCr8

      Range
      266518510..266559633
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039084701.2 → XP_038940629.1  pseudouridylate synthase TRUB1 isoform X2

      UniProtKB/TrEMBL
      A6JI46
      Conserved Domains (1) summary
      cl00130
      Location:73 → 218
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    2. XM_039084721.2 → XP_038940649.1  pseudouridylate synthase TRUB1 isoform X3

      Conserved Domains (1) summary
      cl00130
      Location:61 → 169
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    3. XM_008760538.4 → XP_008758760.1  pseudouridylate synthase TRUB1 isoform X1

      Conserved Domains (2) summary
      TIGR00431
      Location:61 → 282
      TruB; tRNA pseudouridine(55) synthase
      cl00130
      Location:61 → 340
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    4. XM_039084692.2 → XP_038940620.1  pseudouridylate synthase TRUB1 isoform X2

      UniProtKB/TrEMBL
      A6JI46
      Conserved Domains (1) summary
      cl00130
      Location:73 → 218
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    5. XM_039084723.2 → XP_038940651.1  pseudouridylate synthase TRUB1 isoform X4

      Conserved Domains (1) summary
      cl00130
      Location:34 → 179
      PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

    RNA

    1. XR_005489295.2 RNA Sequence

    2. XR_005489288.2 RNA Sequence

    3. XR_005489289.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5M934.1 GenPept UniProtKB/Swiss-Prot:Q5M934

    Gene LinkOut

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