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    Trim13 tripartite motif-containing 13 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 364398, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Trim13provided by RGD
    Official Full Name
    tripartite motif-containing 13provided by RGD
    Primary source
    RGD:1307609
    See related
    Ensembl:ENSRNOG00000009075 AllianceGenome:RGD:1307609
    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 enable transcription coactivator activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including cellular protein metabolic process; defense response to other organism; and negative regulation of viral transcription. Predicted to be located in endoplasmic reticulum membrane and perinuclear endoplasmic reticulum. Predicted to be active in cytoplasm. Orthologous to human TRIM13 (tripartite motif containing 13). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 81.5), Brain (RPKM 38.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    15p12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (39909587..39948719)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (35733548..35772676)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (41897191..41936545)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134482127 Neighboring gene SPRY domain containing 7 Neighboring gene small nucleolar RNA SNORA42/SNORA80 family Neighboring gene potassium channel regulator Neighboring gene uncharacterized LOC134481978

    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. TRIM13 regulates ER stress induced autophagy and clonogenic ability of the cells. Tomar D, et al. Biochim Biophys Acta, 2012 Feb. PMID 22178386
    2. Ret finger protein 2 enhances ionizing radiation-induced apoptosis via degradation of AKT and MDM2. Joo HM, et al. Eur J Cell Biol, 2011 May. PMID 21333377
    3. The RBCC gene RFP2 (Leu5) encodes a novel transmembrane E3 ubiquitin ligase involved in ERAD. Lerner M, et al. Mol Biol Cell, 2007 May. PMID 17314412, Free PMC Article
    4. The Cavβ subunit prevents RFP2-mediated ubiquitination and proteasomal degradation of L-type channels. Altier C, et al. Nat Neurosci, 2011 Feb. PMID 21186355
    5. TRIM protein-mediated regulation of inflammatory and innate immune signaling and its association with antiretroviral activity. Uchil PD, et al. J Virol, 2013 Jan. PMID 23077300, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables transcription coactivator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-like 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
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ERAD pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of viral transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of viral transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of NF-kappaB transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of canonical NF-kappaB signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of canonical NF-kappaB signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of macroautophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of macroautophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein autoubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein autoubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in suppression of viral release by host IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in suppression of viral release by host ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase TRIM13
    Names
    RING-type E3 ubiquitin transferase TRIM13
    putative tumor suppressor RFP2
    ret finger protein 2
    tripartite motif protein 13
    tripartite motif-containing protein 13
    NP_001012210.1
    XP_063130551.1
    XP_063130552.1
    XP_063130553.1
    XP_063130554.1

    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_001012210.1 → NP_001012210.1  E3 ubiquitin-protein ligase TRIM13

      See identical proteins and their annotated locations for NP_001012210.1

      Status: PROVISIONAL

      Source sequence(s)
      BC088425
      UniProtKB/Swiss-Prot
      Q5M7V1
      Related
      ENSRNOP00000092048.1, ENSRNOT00000109510.1
      Conserved Domains (2) summary
      cd16762
      Location:5 → 61
      RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins
      cd19767
      Location:92 → 133
      Bbox2_TRIM13_C-XI; B-box-type 2 zinc finger found in tripartite motif-containing protein 13 (TRIM13) 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_086033.1 Reference GRCr8

      Range
      39909587..39948719
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063274481.1 → XP_063130551.1  E3 ubiquitin-protein ligase TRIM13 isoform X1

      UniProtKB/TrEMBL
      A0A8L2UIK6

    2. XM_063274483.1 → XP_063130553.1  E3 ubiquitin-protein ligase TRIM13 isoform X2

      UniProtKB/Swiss-Prot
      Q5M7V1

    3. XM_063274482.1 → XP_063130552.1  E3 ubiquitin-protein ligase TRIM13 isoform X2

      UniProtKB/Swiss-Prot
      Q5M7V1

    4. XM_063274484.1 → XP_063130554.1  E3 ubiquitin-protein ligase TRIM13 isoform X2

      UniProtKB/Swiss-Prot
      Q5M7V1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5M7V1.1 GenPept UniProtKB/Swiss-Prot:Q5M7V1

    Gene LinkOut

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

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