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

Gene ID: 361775, updated on 2-May-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
Ensembl: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 pseudouridine synthase activity. Predicted to be involved in mRNA pseudouridine synthesis and tRNA modification. Predicted to be located in cytosol and nucleus. Predicted to be active in mitochondrion. Orthologous to human TRUB1 (TruB pseudouridine synthase family member 1). [provided by Alliance of Genome Resources, Apr 2022]
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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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. 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
  3. 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
  4. 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 synthase activity IEA
Inferred from Electronic Annotation
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
  
is_active_in mitochondrion 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, ENSRNOT00000023309.5
    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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