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    Trim59 tripartite motif-containing 59 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 365813, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Trim59provided by RGD
    Official Full Name
    tripartite motif-containing 59provided by RGD
    Primary source
    RGD:1311956
    See related
    EnsemblRapid:ENSRNOG00000010515 AllianceGenome:RGD:1311956
    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
    Also known as
    RGD1311956
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response; negative regulation of canonical NF-kappaB signal transduction; and negative regulation of viral entry into host cell. Predicted to be located in endoplasmic reticulum. Orthologous to human TRIM59 (tripartite motif containing 59). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 342.1), Thymus (RPKM 203.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Trim59 in Genome Data Viewer
    Location:
    2q32
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (155579183..155593450, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (153269210..153281185, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (165629903..165641751, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene microRNA 15b Neighboring gene structural maintenance of chromosomes 4 Neighboring gene microRNA 16 Neighboring gene karyopherin subunit alpha 4 Neighboring gene small Cajal body-specific RNA 7 Neighboring gene guanine nucleotide exchange factor MSS4-like Neighboring gene TOX high mobility group box family member 3 like 1

    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. A role of TRIM59 in pulmonary hypertension: modulating the protein ubiquitylation modification. Liu Y, et al. J Transl Med, 2023 Nov 17. PMID 37978515, Free PMC Article
    2. TRIM59 interacts with ECSIT and negatively regulates NF-κB and IRF-3/7-mediated signal pathways. Kondo T, et al. Biochem Biophys Res Commun, 2012 Jun 8. PMID 22588174
    3. TRIM E3 ligases interfere with early and late stages of the retroviral life cycle. Uchil PD, et al. PLoS Pathog, 2008 Feb 8. PMID 18248090, 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

    What's a GeneRIF?
    1. A role of TRIM59 in pulmonary hypertension: modulating the protein ubiquitylation modification.
      Title: A role of TRIM59 in pulmonary hypertension: modulating the protein ubiquitylation modification.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of canonical NF-kappaB signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of viral entry into host cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT part_of intraciliary transport particle B IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tripartite motif-containing protein 59
    NP_001102415.1
    XP_006232546.1
    XP_006232547.1

    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_001108945.1 → NP_001102415.1  tripartite motif-containing protein 59

      See identical proteins and their annotated locations for NP_001102415.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473976
      UniProtKB/TrEMBL
      B5DF13, F7EYS6
      Conserved Domains (2) summary
      cd16763
      Location:5 → 60
      RING-HC_TRIM59_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins
      cd19790
      Location:95 → 134
      Bbox2_TRIM59_C-XI; B-box-type 2 zinc finger found in tripartite motif-containing protein 59 (TRIM59) and similar proteins

    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_086020.1 Reference GRCr8

      Range
      155579183..155593450 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006232484.5 → XP_006232546.1  tripartite motif-containing protein 59 isoform X1

      See identical proteins and their annotated locations for XP_006232546.1

      UniProtKB/TrEMBL
      B5DF13, F7EYS6
      Related
      ENSRNOP00000111836.1, ENSRNOT00000171616.1
      Conserved Domains (2) summary
      cd16763
      Location:5 → 60
      RING-HC_TRIM59_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins
      cd19790
      Location:95 → 134
      Bbox2_TRIM59_C-XI; B-box-type 2 zinc finger found in tripartite motif-containing protein 59 (TRIM59) and similar proteins

    2. XM_006232485.5 → XP_006232547.1  tripartite motif-containing protein 59 isoform X1

      See identical proteins and their annotated locations for XP_006232547.1

      UniProtKB/TrEMBL
      B5DF13, F7EYS6
      Related
      ENSRNOP00000013987.3, ENSRNOT00000013987.5
      Conserved Domains (2) summary
      cd16763
      Location:5 → 60
      RING-HC_TRIM59_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins
      cd19790
      Location:95 → 134
      Bbox2_TRIM59_C-XI; B-box-type 2 zinc finger found in tripartite motif-containing protein 59 (TRIM59) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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