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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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