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    Trim5 tripartite motif-containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308906, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Trim5provided by RGD
    Official Full Name
    tripartite motif-containing 5provided by RGD
    Primary source
    RGD:1304579
    See related
    Ensembl:ENSRNOG00000017191 AllianceGenome:RGD:1304579
    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
    RGD1304579
    Summary
    Predicted to enable several functions, including protein homodimerization activity; transcription coactivator activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of NF-kappaB transcription factor activity; and regulation of signal transduction. Predicted to be located in P-body. Predicted to be active in cytosol and nucleoplasm. Predicted to colocalize with omegasome. Orthologous to human TRIM5 (tripartite motif containing 5). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 314.2), Thymus (RPKM 258.3) and 9 other tissues See more
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    Genomic context

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    See Trim5 in Genome Data Viewer
    Location:
    1q32
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (168132277..168149263, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (158720407..158737393, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (169446774..169463760, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 6 Neighboring gene tripartite motif-containing 34 Neighboring gene tripartite motif-containing 30A like, pseudogene 1 Neighboring gene tripartite motif-containing 30C Neighboring gene G3BP stress granule assembly factor 1, pseudogene 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
    • 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. p62/sequestosome-1 associates with and sustains the expression of retroviral restriction factor TRIM5alpha. O'Connor C, et al. J Virol, 2010 Jun. PMID 20357094, Free PMC Article
    2. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. Xu L, et al. Exp Cell Res, 2003 Aug 1. PMID 12878161
    3. Unique features of TRIM5alpha among closely related human TRIM family members. Li X, et al. Virology, 2007 Apr 10. PMID 17156811
    4. TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Pertel T, et al. Nature, 2011 Apr 21. PMID 21512573, Free PMC Article
    5. TRIM27 negatively regulates NOD2 by ubiquitination and proteasomal degradation. Zurek B, et al. PLoS One, 2012. PMID 22829933, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables pattern recognition receptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-macromolecule adaptor activity ISO
    Inferred from Sequence Orthology
    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-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 activation of innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagy 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of viral entry into host cell 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 MAPK cascade ISO
    Inferred from Sequence Orthology
    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 autophagy 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K63-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of lipopolysaccharide-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of viral entry into host cell IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in suppression of viral release by host ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in omegasome ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    tripartite motif-containing protein 5
    NP_001014045.1
    XP_006229974.1
    XP_038934094.1
    XP_063119050.1

    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_001014023.1 → NP_001014045.1  tripartite motif-containing protein 5

      See identical proteins and their annotated locations for NP_001014045.1

      Status: PROVISIONAL

      Source sequence(s)
      BC078926
      UniProtKB/TrEMBL
      A0A0G2K6C7, F7FKX1, Q6AYT1
      Related
      ENSRNOP00000023099.4, ENSRNOT00000023100.6
      Conserved Domains (4) summary
      smart00336
      Location:92 → 132
      BBOX; B-Box-type zinc finger
      cd15822
      Location:290 → 507
      SPRY_PRY_TRIM5; PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger protein 88 (RNF88)
      cl17238
      Location:15 → 58
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      cl21478
      Location:132 → 231
      ATP-synt_B; ATP synthase B/B' CF(0)

    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_086019.1 Reference GRCr8

      Range
      168132277..168149263 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006229912.5 → XP_006229974.1  tripartite motif-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_006229974.1

      UniProtKB/TrEMBL
      A0A0G2K6C7, F7FKX1, Q6AYT1
      Conserved Domains (4) summary
      smart00336
      Location:92 → 132
      BBOX; B-Box-type zinc finger
      cd15822
      Location:290 → 507
      SPRY_PRY_TRIM5; PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger protein 88 (RNF88)
      cl17238
      Location:15 → 58
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      cl21478
      Location:132 → 231
      ATP-synt_B; ATP synthase B/B' CF(0)

    2. XM_039078166.1 → XP_038934094.1  tripartite motif-containing protein 5 isoform X2

      Conserved Domains (1) summary
      cd15822
      Location:47 → 264
      SPRY_PRY_TRIM5; PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger protein 88 (RNF88)

    3. XM_063262980.1 → XP_063119050.1  tripartite motif-containing protein 5 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version

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