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

Gene ID: 79263, updated on 11-Apr-2024

Summary

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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 act upstream of or within apoptotic process. Predicted to be located in cytosol; mitochondrion; and nucleus. Predicted to be active in cytoplasm. Is expressed in several structures, including brain; cardiovascular system; genitourinary system; gut; and immune system. Orthologous to human TRIM39 (tripartite motif containing 39). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 12.6), CNS E14 (RPKM 11.4) and 28 other tissues See more
Orthologs
human all
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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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 (17) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

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

General gene information

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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 metal ion binding IEA
Inferred from Electronic Annotation
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
acts_upstream_of_or_within apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic G2 DNA damage checkpoint signaling ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of canonical NF-kappaB signal transduction ISO
Inferred from Sequence Orthology
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 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 ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cell cycle G1/S phase transition ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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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)

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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_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

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