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    Trim39 tripartite motif-containing 39 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309591, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Trim39provided by RGD
    Official Full Name
    tripartite motif-containing 39provided by RGD
    Primary source
    RGD:1303115
    See related
    Ensembl:ENSRNOG00000000785 AllianceGenome:RGD:1303115
    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
    Also known as
    Rnf23
    Summary
    Predicted to enable identical protein binding activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle phase transition; and regulation of signal transduction. Predicted to be located in cytosol; mitochondrion; and nucleus. Predicted to be active in cytoplasm. Orthologous to human TRIM39 (tripartite motif containing 39). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 106.4), Spleen (RPKM 68.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Trim39 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (2008528..2022383)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (2003320..2017175)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (2500691..2514546)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene ribonuclease P/MRP subunit p21 Neighboring gene RT1 class I, locus M10, gene 1 Neighboring gene RT1 class pseudogene 3082ex4-5 Neighboring gene RT1 class I, locus P2, pseudogene 1 Neighboring gene Riken clone 5830469G19 related pseudogene 40

    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. TRIM39 negatively regulates the NFκB-mediated signaling pathway through stabilization of Cactin. Suzuki M, et al. Cell Mol Life Sci, 2016 Mar. PMID 26363554, Free PMC Article
    2. TRIM39 is a MOAP-1-binding protein that stabilizes MOAP-1 through inhibition of its poly-ubiquitination process. Lee SS, et al. Exp Cell Res, 2009 Apr 15. PMID 19100260
    3. TRIM39 regulates cell cycle progression and DNA damage responses via stabilizing p21. Zhang L, et al. Proc Natl Acad Sci U S A, 2012 Dec 18. PMID 23213251, Free PMC Article
    4. Systematic analysis of dimeric E3-RING interactions reveals increased combinatorial complexity in human ubiquitination networks. Woodsmith J, et al. Mol Cell Proteomics, 2012 Jul. PMID 22493164, Free PMC Article
    5. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, et al. Genome Res, 2004 Apr. PMID 15060004, Free PMC Article

    See all (9) 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic G2 DNA damage checkpoint signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic G2 DNA damage checkpoint signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitotic G2 DNA damage checkpoint signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of canonical NF-kappaB signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of canonical NF-kappaB signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of canonical NF-kappaB signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in phosphorelay signal transduction system IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of apoptotic signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of apoptotic signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein stabilization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein stabilization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein stabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell cycle G1/S phase transition IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell cycle G1/S phase transition ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell cycle G1/S phase transition ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase TRIM39
    Names
    RING finger protein 23
    RING-type E3 ubiquitin transferase TRIM39
    tripartite motif protein 39
    tripartite motif-containing protein 39
    NP_998727.1

    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_213562.1 → NP_998727.1  E3 ubiquitin-protein ligase TRIM39

      See identical proteins and their annotated locations for NP_998727.1

      Status: VALIDATED

      Source sequence(s)
      BX883050
      UniProtKB/Swiss-Prot
      Q6MFZ5
      UniProtKB/TrEMBL
      A0A8L2PYM6, A6KR95
      Related
      ENSRNOP00000094860.1, ENSRNOT00000118924.1
      Conserved Domains (4) summary
      PRK02224
      Location:144 → 271
      PRK02224; DNA double-strand break repair Rad50 ATPase
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cd19780
      Location:103 → 146
      Bbox2_TRIM39-like; B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 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_086038.1 Reference GRCr8

      Range
      2008528..2022383
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6MFZ5.1 GenPept UniProtKB/Swiss-Prot:Q6MFZ5

    Gene LinkOut

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

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