U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Trim39 tripartite motif-containing 39 [ Mus musculus (house mouse) ]

    Gene ID: 79263, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Trim39provided by MGI
    Official Full Name
    tripartite motif-containing 39provided by MGI
    Primary source
    MGI:MGI:1890659
    See related
    Ensembl:ENSMUSG00000045409 AllianceGenome:MGI:1890659
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    tfp; Rnf23; mKIAA4179; RBCC-B30.2; 1100001D15Rik; E130103K13Rik
    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 mitochondrion and nucleus. Predicted to be active in cytosol. Is expressed in several structures, including cardiovascular system; central nervous system; genitourinary system; gut; and immune system. Orthologous to human TRIM39 (tripartite motif containing 39). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 12.6), CNS E14 (RPKM 11.4) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Trim39 in Genome Data Viewer
    Location:
    17 B1; 17 19.01 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (36569764..36582896, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (36258872..36272004, complement)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene non-histone chromosomal protein HMG-14 pseudogene Neighboring gene ribonuclease P 21 subunit Neighboring gene STARR-seq mESC enhancer starr_42489 Neighboring gene histocompatibility 2, M region locus 10.2 Neighboring gene predicted gene, 33257

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Molecular cloning of testis-abundant finger Protein/Ring finger protein 23 (RNF23), a novel RING-B box-coiled coil-B30.2 protein on the class I region of the human MHC. Orimo A, et al. Biochem Biophys Res Commun, 2000 Sep 16. PMID 11006080
    2. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, et al. Science, 2004 Dec 24. PMID 15618518
    3. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Koscielny G, et al. Nucleic Acids Res, 2014 Jan. PMID 24194600, Free PMC Article
    4. GUDMAP: the genitourinary developmental molecular anatomy project. McMahon AP, et al. J Am Soc Nephrol, 2008 Apr. PMID 18287559
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2) 

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • KIAA4179

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    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 innate immune response IBA
    Inferred from Biological aspect of Ancestor
    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 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 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 positive regulation of apoptotic signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein ubiquitination 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
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    E3 ubiquitin-protein ligase TRIM39
    Names
    RING-B box-coiled-coil-B30.2
    RING-type E3 ubiquitin transferase TRIM39
    ring finger protein 23
    testis-abundant finger protein
    tripartite motif-containing protein 39
    NP_001344818.1
    NP_001361535.1
    NP_077788.2
    NP_840065.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001357889.1 → NP_001344818.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC129554, AK053507
      Related
      ENSMUST00000113704.10
      Conserved Domains (3) summary
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cl21478
      Location:177 → 246
      ATP-synt_B; ATP synthase B/B' CF(0)
      cl28410
      Location:20 → 179
      RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

    2. NM_001374606.1 → NP_001361535.1  E3 ubiquitin-protein ligase TRIM39 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC129554
      UniProtKB/Swiss-Prot
      Q8BPR5, Q8K0F7, Q9ESN2
      UniProtKB/TrEMBL
      G3UWI0
      Related
      ENSMUSP00000133298.2, ENSMUST00000173369.2
      Conserved Domains (4) summary
      PRK02224
      Location:144 → 294
      PRK02224; DNA double-strand break repair Rad50 ATPase
      cd13745
      Location:314 → 491
      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

    3. NM_024468.2 → NP_077788.2  E3 ubiquitin-protein ligase TRIM39 isoform 1

      See identical proteins and their annotated locations for NP_077788.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AB046382, AK220298
      Consensus CDS
      CCDS37611.1
      UniProtKB/Swiss-Prot
      Q8BPR5, Q8K0F7, Q9ESN2
      UniProtKB/TrEMBL
      E9QLN4
      Related
      ENSMUSP00000039790.7, ENSMUST00000042717.13
      Conserved Domains (4) summary
      cd00021
      Location:106 → 143
      BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
      pfam15227
      Location:29 → 69
      zf-C3HC4_4; zinc finger of C3HC4-type, RING
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cl23765
      Location:151 → 272
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    4. NM_178281.1 → NP_840065.1  E3 ubiquitin-protein ligase TRIM39 isoform 1

      See identical proteins and their annotated locations for NP_840065.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK220298, BY312131
      Consensus CDS
      CCDS37611.1
      UniProtKB/Swiss-Prot
      Q8BPR5, Q8K0F7, Q9ESN2
      UniProtKB/TrEMBL
      E9QLN4
      Related
      ENSMUSP00000109336.4, ENSMUST00000113706.10
      Conserved Domains (4) summary
      cd00021
      Location:106 → 143
      BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
      pfam15227
      Location:29 → 69
      zf-C3HC4_4; zinc finger of C3HC4-type, RING
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cl23765
      Location:151 → 272
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      36569764..36582896 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ESN2.1 GenPept UniProtKB/Swiss-Prot:Q9ESN2

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous