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    Tsen54 tRNA splicing endonuclease subunit 54 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 690308, updated on 17-Aug-2024

    Summary

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    Official Symbol
    Tsen54provided by RGD
    Official Full Name
    tRNA splicing endonuclease subunit 54provided by RGD
    Primary source
    RGD:1597379
    See related
    EnsemblRapid:ENSRNOG00000004598 AllianceGenome:RGD:1597379
    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 be involved in tRNA-type intron splice site recognition and cleavage. Predicted to be part of tRNA-intron endonuclease complex. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2A; pontocerebellar hypoplasia type 4; and pontocerebellar hypoplasia type 5. Orthologous to human TSEN54 (tRNA splicing endonuclease subunit 54). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 26.8), Muscle (RPKM 26.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    10q32.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (101540479..101549022)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (101041607..101050088)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (104358401..104366926)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 94 Neighboring gene microRNA 3577 Neighboring gene cask-interacting protein 2 Neighboring gene LLGL scribble cell polarity complex component 2 Neighboring gene myosin XVB

    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 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. Handling tRNA introns, archaeal way and eukaryotic way. Yoshihisa T. Front Genet, 2014. PMID 25071838, Free PMC Article
    2. The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs. Weitzer S, et al. Nature, 2007 May 10. PMID 17495927
    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

    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA-type intron splice site recognition and cleavage IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of tRNA-intron endonuclease complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    tRNA-splicing endonuclease subunit Sen54
    Names
    TSEN54 tRNA splicing endonuclease subunit
    tRNA splicing endonuclease 54 homolog

    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_001109576.1 → NP_001103046.1  tRNA-splicing endonuclease subunit Sen54

      See identical proteins and their annotated locations for NP_001103046.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473948
      UniProtKB/TrEMBL
      A0A8I6AEJ0, A6HKQ9, D3ZZT6
      Conserved Domains (1) summary
      pfam12928
      Location:63 → 130
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    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_086028.1 Reference GRCr8

      Range
      101540479..101549022
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039086874.2 → XP_038942802.1  tRNA-splicing endonuclease subunit Sen54 isoform X1

      Conserved Domains (2) summary
      pfam12928
      Location:67 → 134
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term
      cl40623
      Location:120 → 191
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    2. XM_039086876.2 → XP_038942804.1  tRNA-splicing endonuclease subunit Sen54 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AEJ0
      Related
      ENSRNOP00000091908.2, ENSRNOT00000098924.2
      Conserved Domains (2) summary
      pfam12928
      Location:67 → 134
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term
      cl40623
      Location:120 → 191
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    3. XM_039086875.2 → XP_038942803.1  tRNA-splicing endonuclease subunit Sen54 isoform X3

      Conserved Domains (2) summary
      pfam12928
      Location:67 → 134
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term
      cl40623
      Location:120 → 173
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    4. XM_006247737.5 → XP_006247799.1  tRNA-splicing endonuclease subunit Sen54 isoform X2

      Related
      ENSRNOP00000111015.1, ENSRNOT00000137395.1
      Conserved Domains (1) summary
      pfam12928
      Location:63 → 130
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    5. XM_063269886.1 → XP_063125956.1  tRNA-splicing endonuclease subunit Sen54 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AEJ0
      Related
      ENSRNOP00000006327.3, ENSRNOT00000006327.6

    RNA

    1. XR_005489949.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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