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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

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