U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Tsen54 tRNA splicing endonuclease subunit 54 [ Mus musculus (house mouse) ]

    Gene ID: 76265, updated on 9-May-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Tsen54provided by MGI
    Official Full Name
    tRNA splicing endonuclease subunit 54provided by MGI
    Primary source
    MGI:MGI:1923515
    See related
    Ensembl:ENSMUSG00000020781 AllianceGenome:MGI:1923515
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    0610034P02Rik
    Summary
    Predicted to be involved in tRNA-type intron splice site recognition and cleavage. Predicted to act upstream of or within mRNA processing and tRNA processing. Predicted to be located in nucleus. Predicted to be part of tRNA-intron endonuclease complex. Is expressed in cerebellum; retina inner nuclear layer; and retina outer nuclear layer. 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
    Ubiquitous expression in duodenum adult (RPKM 11.3), ovary adult (RPKM 11.0) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Tsen54 in Genome Data Viewer
    Location:
    11 E2; 11 80.91 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (115704563..115713928)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (115813728..115823102)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene transmembrane protein 94 Neighboring gene microRNA 5621 Neighboring gene CASK-interacting protein 2 Neighboring gene STARR-positive B cell enhancer ABC_E3039 Neighboring gene STARR-seq mESC enhancer starr_31175 Neighboring gene LLGL2 scribble cell polarity complex component Neighboring gene STARR-seq mESC enhancer starr_31178 Neighboring gene myosin XVB Neighboring gene RecQ protein-like 5

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Three-Dimensional X-ray Imaging of β-Galactosidase Reporter Activity by Micro-CT: Implication for Quantitative Analysis of Gene Expression. Ermakova O, et al. Brain Sci, 2021 Jun 4. PMID 34199780, Free PMC Article
    2. Three-dimensional microCT imaging of murine embryonic development from immediate post-implantation to organogenesis: application for phenotyping analysis of early embryonic lethality in mutant animals. Ermakova O, et al. Mamm Genome, 2018 Apr. PMID 29170794, Free PMC Article
    3. Ash2l interacts with Tbx1 and is required during early embryogenesis. Stoller JZ, et al. Exp Biol Med (Maywood), 2010 May. PMID 20463296, Free PMC Article
    4. Genomic analysis of mouse retinal development. Blackshaw S, et al. PLoS Biol, 2004 Sep. PMID 15226823, Free PMC Article
    5. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2)  1 citation

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within tRNA processing IEA
    Inferred from Electronic Annotation
    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
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of tRNA-intron endonuclease complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    tRNA-splicing endonuclease subunit Sen54
    Names
    likely ortholog of H. sapiens SEN54L
    tRNA splicing endonuclease 54 homolog
    tRNA-intron endonuclease Sen54

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_029557.1 → NP_083833.1  tRNA-splicing endonuclease subunit Sen54

      See identical proteins and their annotated locations for NP_083833.1

      Status: VALIDATED

      Source sequence(s)
      AK002758, BB273422, BY203746
      Consensus CDS
      CCDS25648.1
      UniProtKB/Swiss-Prot
      B1ATA4, B1ATA5, Q8C2A2, Q9DCI5
      Related
      ENSMUSP00000021134.4, ENSMUST00000021134.10
      Conserved Domains (1) summary
      pfam12928
      Location:63 → 130
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      115704563..115713928
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006534415.4 → XP_006534478.1  tRNA-splicing endonuclease subunit Sen54 isoform X1

      See identical proteins and their annotated locations for XP_006534478.1

      Conserved Domains (2) summary
      PRK09297
      Location:181 → 252
      PRK09297; tRNA-splicing endonuclease subunit alpha; Reviewed
      pfam12928
      Location:128 → 195
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    2. XM_006534419.4 → XP_006534482.1  tRNA-splicing endonuclease subunit Sen54 isoform X2

      Conserved Domains (2) summary
      PRK09297
      Location:181 → 234
      PRK09297; tRNA-splicing endonuclease subunit alpha; Reviewed
      pfam12928
      Location:128 → 195
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    3. XM_006534417.4 → XP_006534480.1  tRNA-splicing endonuclease subunit Sen54 isoform X1

      See identical proteins and their annotated locations for XP_006534480.1

      Conserved Domains (2) summary
      PRK09297
      Location:181 → 252
      PRK09297; tRNA-splicing endonuclease subunit alpha; Reviewed
      pfam12928
      Location:128 → 195
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    4. XM_036157059.1 → XP_036012952.1  tRNA-splicing endonuclease subunit Sen54 isoform X3

      Conserved Domains (2) summary
      pfam12928
      Location:81 → 148
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term
      cl40623
      Location:134 → 187
      tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term

    RNA

    1. XR_879757.4 RNA Sequence

    2. XR_004937055.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C2A2.2 GenPept UniProtKB/Swiss-Prot:Q8C2A2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous