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trub1 TruB pseudouridine (psi) synthase family member 1 [ Danio rerio (zebrafish) ]

Gene ID: 556642, updated on 2-Nov-2024

Summary

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Official Symbol
trub1provided by ZNC
Official Full Name
TruB pseudouridine (psi) synthase family member 1provided by ZNC
Primary source
ZFIN:ZDB-GENE-080723-73
See related
Ensembl:ENSDARG00000053805 AllianceGenome:ZFIN:ZDB-GENE-080723-73
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:195155
Summary
Predicted to enable pseudouridine synthase activity. Predicted to be involved in mRNA pseudouridine synthesis and tRNA modification. Predicted to act upstream of or within pseudouridine synthesis and tRNA processing. Predicted to be active in nucleus. Orthologous to human TRUB1 (TruB pseudouridine synthase family member 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See trub1 in Genome Data Viewer
Location:
chromosome: 12
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 12 NC_007123.7 (30036706..30043898, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 12 NC_007123.6 (29921804..29928996, complement)

Chromosome 12 - NC_007123.7Genomic Context describing neighboring genes Neighboring gene gdnf family receptor alpha 1b Neighboring gene attractin-like 1b Neighboring gene actin binding LIM protein 1b Neighboring gene uncharacterized LOC108191726 Neighboring gene actin filament associated protein 1-like 2 Neighboring gene kelch repeat and BTB domain-containing protein 13

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. tdrd1 is a germline-specific and sexually dimorphically expressed gene in Paralichthys olivaceus. Zhao J, et al. Gene, 2018 Oct 5. PMID 29920365
  2. Gdnf Acts as a Germ Cell-Derived Growth Factor and Regulates the Zebrafish Germ Stem Cell Niche in Autocrine- and Paracrine-Dependent Manners. Doretto LB, et al. Cells, 2022 Apr 11. PMID 35455974, Free PMC Article
  3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, 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 ZFIN

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables pseudouridine synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 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
acts_upstream_of_or_within RNA modification IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within RNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within pseudouridine synthesis IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA modification IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within tRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
pseudouridylate synthase TRUB1
Names
TruB pseudouridine (psi) synthase homolog 1
NP_001122159.1

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_001128687.1 → NP_001122159.1  pseudouridylate synthase TRUB1

    See identical proteins and their annotated locations for NP_001122159.1

    Status: PROVISIONAL

    Source sequence(s)
    BC163184
    UniProtKB/TrEMBL
    B3DHG0, B3DIM3
    Related
    ENSDARP00000070369.4, ENSDART00000075889.6
    Conserved Domains (2) summary
    TIGR00431
    Location:20 → 236
    TruB; tRNA pseudouridine(55) synthase
    cl00130
    Location:20 → 279
    PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007123.7 Reference GRCz11 Primary Assembly

    Range
    30036706..30043898 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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