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    Trim65 tripartite motif-containing 65 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303684, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Trim65provided by RGD
    Official Full Name
    tripartite motif-containing 65provided by RGD
    Primary source
    RGD:1559497
    See related
    EnsemblRapid:ENSRNOG00000024145 AllianceGenome:RGD:1559497
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in negative regulation of inflammatory response; positive regulation of autophagy; and protein polyubiquitination. Predicted to act upstream of or within several processes, including innate immune response; positive regulation of protein oligomerization; and positive regulation of type I interferon production. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in cytoplasm. Orthologous to human TRIM65 (tripartite motif containing 65). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 51.5), Heart (RPKM 50.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Trim65 in Genome Data Viewer
    Location:
    10q32.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (101847822..101863052, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (101357937..101364036, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (104674956..104681055, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102552044 Neighboring gene WW domain binding protein 2 Neighboring gene uncharacterized LOC120093105 Neighboring gene tripartite motif-containing 47 Neighboring gene mitochondrial ribosomal protein L38 Neighboring gene Fas binding factor 1 Neighboring gene small Cajal body-specific RNA 4

    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
    • 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. TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity. Kimura T, et al. J Cell Biol, 2015 Sep 14. PMID 26347139, Free PMC Article
    2. 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

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin-protein transferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within antiviral innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of interferon-alpha production ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of interferon-beta production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interferon-beta production ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of protein oligomerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K48-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K63-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within type I interferon-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase TRIM65
    Names
    tripartite motif-containing protein 65
    NP_001129186.1
    XP_063125308.1
    XP_063125309.1

    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_001135714.2 → NP_001129186.1  E3 ubiquitin-protein ligase TRIM65

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      D3ZY16
      Related
      ENSRNOP00000047932.4, ENSRNOT00000046026.7
      Conserved Domains (4) summary
      cd12896
      Location:319 → 500
      SPRY_PRY_TRIM65; PRY/SPRY domain in tripartite motif-containing domain 65 (TRIM65)
      cd00162
      Location:13 → 51
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      cl00034
      Location:89 → 130
      Bbox_SF; B-box-type zinc finger superfamily
      cl17238
      Location:11 → 52
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    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
      101847822..101863052 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269238.1 → XP_063125308.1  E3 ubiquitin-protein ligase TRIM65 isoform X1

    2. XM_063269239.1 → XP_063125309.1  E3 ubiquitin-protein ligase TRIM65 isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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