TRIM38 Gene (Protein Coding)

Tripartite Motif Containing 38

GC06P025962
GIFtS:
39
This gene encodes a member of the tripartite motif (TRIM) family. The encoded protein contains a RING-type zinc finger, B box-type zinc finger and SPRY domain. The function of this protein has not been identified. A pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Jul 2012] See more...

Aliases for TRIM38 Gene

Aliases for TRIM38 Gene

  • Tripartite Motif Containing 38 2 3 5
  • RORET 2 3 4
  • RING-Type E3 Ubiquitin Transferase TRIM38 3 4
  • Tripartite Motif-Containing Protein 38 3 4
  • E3 Ubiquitin-Protein Ligase TRIM38 3 4
  • Zinc Finger Protein RoRet 3 4
  • Ring Finger Protein 15 2 3
  • RNF15 3 4
  • Ro/SSA Ribonucleoprotein Homolog 3
  • Tripartite Motif-Containing 38 2
  • RING Finger Protein 15 4
  • EC 2.3.2.27 4
  • TRIM38 5

External Ids for TRIM38 Gene

Previous HGNC Symbols for TRIM38 Gene

  • RNF15

Previous GeneCards Identifiers for TRIM38 Gene

  • GC06P026006
  • GC06P026071
  • GC06P026070
  • GC06P025906
  • GC06P025965
  • GC06P025966
  • GC06P025967
  • GC06P025968
  • GC06P025969

Summaries for TRIM38 Gene

Entrez Gene Summary for TRIM38 Gene

  • This gene encodes a member of the tripartite motif (TRIM) family. The encoded protein contains a RING-type zinc finger, B box-type zinc finger and SPRY domain. The function of this protein has not been identified. A pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Jul 2012]

GeneCards Summary for TRIM38 Gene

TRIM38 (Tripartite Motif Containing 38) is a Protein Coding gene. Diseases associated with TRIM38 include Fanconi Renotubular Syndrome 2. Among its related pathways are Innate Immune System and Interferon gamma signaling. Gene Ontology (GO) annotations related to this gene include ligase activity and obsolete signal transducer activity. An important paralog of this gene is TRIM21.

UniProtKB/Swiss-Prot Summary for TRIM38 Gene

  • E3 ubiquitin-protein ligase. Mediates 'Lys-48'-linked polyubiquitination and proteasomal degradation of the critical TLR adapter TICAM1, inhibiting TLR3-mediated type I interferon signaling.

Additional gene information for TRIM38 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRIM38 Gene

Genomics for TRIM38 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TRIM38 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRIM38 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRIM38

Top Transcription factor binding sites by QIAGEN in the TRIM38 gene promoter:
  • Bach2
  • HNF-4alpha1
  • Nkx6-1
  • PPAR-alpha
  • PPAR-gamma1
  • PPAR-gamma2
  • STAT5B
  • XBP-1

Genomic Locations for TRIM38 Gene

Latest Assembly
chr6:25,962,723-25,991,231
(GRCh38/hg38)
Size:
28,509 bases
Orientation:
Plus strand

Previous Assembly
chr6:25,963,030-25,991,459
(GRCh37/hg19 by Entrez Gene)
Size:
28,430 bases
Orientation:
Plus strand

chr6:25,963,030-25,987,384
(GRCh37/hg19 by Ensembl)
Size:
24,355 bases
Orientation:
Plus strand

Genomic View for TRIM38 Gene

Genes around TRIM38 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM38 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM38 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRIM38 Gene

Proteins for TRIM38 Gene

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  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for TRIM38 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00635-TRI38_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase TRIM38
    Protein Accession:
    O00635
    Secondary Accessions:
    • B2R862

    Protein attributes for TRIM38 Gene

    Size:
    465 amino acids
    Molecular mass:
    53416 Da
    Quaternary structure:
    No Data Available

neXtProt entry for TRIM38 Gene

Protein Expression for TRIM38 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRIM38 Gene

  • Ubiquitination at Lys122, Lys137, and Lys227
  • Modification sites at PhosphoSitePlus

Other Protein References for TRIM38 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TRIM38 Gene

Domains & Families for TRIM38 Gene

Gene Families for TRIM38 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for TRIM38 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • Butyrophylin C-terminal DUF signature
  • SPRY-associated domain
  • B-box zinc finger signature
ProtoNet:

Suggested Antigen Peptide Sequences for TRIM38 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger protein RoRet (TRI38_HUMAN)
genes like me logo Genes that share domains with TRIM38: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TRIM38 Gene

Function for TRIM38 Gene

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  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for TRIM38 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase. Mediates 'Lys-48'-linked polyubiquitination and proteasomal degradation of the critical TLR adapter TICAM1, inhibiting TLR3-mediated type I interferon signaling.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;.

Enzyme Numbers (IUBMB) for TRIM38 Gene

Phenotypes From GWAS Catalog for TRIM38 Gene

Gene Ontology (GO) - Molecular Function for TRIM38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IDA 23077300
GO:0005515 protein binding IPI 23275563
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0019901 protein kinase binding IBA 21873635
genes like me logo Genes that share ontologies with TRIM38: view
genes like me logo Genes that share phenotypes with TRIM38: view

Animal Models for TRIM38 Gene

MGI Knock Outs for TRIM38:
  • Trim38 Trim38<tm1(KOMP)Vlcg>

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM38

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRIM38 Gene

Localization for TRIM38 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRIM38 gene
Compartment Confidence
nucleus 4
cytosol 4
plasma membrane 2
cytoskeleton 2
lysosome 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Centrosome (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRIM38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005654 nucleoplasm IBA 21873635
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with TRIM38: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TRIM38 Gene

Pathways & Interactions for TRIM38 Gene

genes like me logo Genes that share pathways with TRIM38: view

Pathways by source for TRIM38 Gene

UniProtKB/Swiss-Prot O00635-TRI38_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for TRIM38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IBA 21873635
GO:0002376 immune system process IEA --
GO:0010468 regulation of gene expression IBA 21873635
GO:0010508 positive regulation of autophagy IBA 21873635
GO:0016567 protein ubiquitination IBA 21873635
genes like me logo Genes that share ontologies with TRIM38: view

No data available for SIGNOR curated interactions for TRIM38 Gene

Drugs & Compounds for TRIM38 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for TRIM38 Gene

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  2. miRNA products for research
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  4. Clone products for research

mRNA/cDNA for TRIM38 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM38

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM38 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b
SP1: - -
SP2: -
SP3:
SP4: - -
SP5: - - -
SP6: -
SP7: - -
SP8:

Relevant External Links for TRIM38 Gene

GeneLoc Exon Structure for
TRIM38

Expression for TRIM38 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRIM38 Gene

mRNA expression in normal human tissues for TRIM38 Gene
mRNA expression by BioGPS for TRIM38 GenemRNA expression by GTEx for TRIM38 Gene

mRNA differential expression in normal tissues according to GTEx for TRIM38 Gene

This gene is overexpressed in Whole Blood (x4.7).

Protein differential expression in normal tissues from HIPED for TRIM38 Gene

This gene is overexpressed in Bone marrow stromal cell (15.5), Lymph node (12.0), and Peripheral blood mononuclear cells (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRIM38 Gene



Protein tissue co-expression partners for TRIM38 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRIM38

SOURCE GeneReport for Unigene cluster for TRIM38 Gene:

Hs.584851

mRNA Expression by UniProt/SwissProt for TRIM38 Gene:

O00635-TRI38_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for TRIM38 Gene

  • Lung(4.4)
  • Liver(4.3)
  • Spleen(2.4)
  • Kidney(2.4)
  • Lymph node(2.1)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with TRIM38: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM38 Gene

Orthologs for TRIM38 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRIM38 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TRIM38 30 31
  • 99.14 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TRIM38 30 31
  • 84.24 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TRIM38 30 31
  • 81.15 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Trim38 30 17 31
  • 69.86 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia LOC680019 30
  • 64.04 (n)
Chicken
(Gallus gallus)
 Aves -- 31
  • 35 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 35 (a)
 OneToMany
Species where no ortholog for TRIM38 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for TRIM38 Gene

ENSEMBL:
Gene Tree for TRIM38 (if available)
TreeFam:
Gene Tree for TRIM38 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRIM38: view image

Paralogs for TRIM38 Gene

Paralogs for TRIM38 Gene

(29) SIMAP similar genes for TRIM38 Gene using alignment to 1 proteins:

  • TRI38_HUMAN

Pseudogenes.org Pseudogenes for TRIM38 Gene

genes like me logo Genes that share paralogs with TRIM38: view

Variants for TRIM38 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRIM38 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs10317 - p.Gly421Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRIM38 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TRIM38 Gene

Variant ID Type Subtype PubMed ID
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for TRIM38 Gene

Residual Variation Intolerance Score: 78.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.32; 63.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRIM38 Gene

Human Gene Mutation Database (HGMD)
TRIM38
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM38

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM38 Gene

Disorders for TRIM38 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TRIM38 Gene - From: COP

Disorder Aliases PubMed IDs
fanconi renotubular syndrome 2
  • frts2
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRIM38

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TRIM38: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRIM38 Gene

Publications for TRIM38 Gene

  1. TRIM38 negatively regulates TLR3-mediated IFN-β signaling by targeting TRIF for degradation. (PMID: 23056470) Xue Q … Hung T (PloS one 2012) 3 4
  2. Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels. (PMID: 19084217) Benyamin B … Visscher PM (American journal of human genetics 2009) 3 41
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. A 1.1-Mb transcript map of the hereditary hemochromatosis locus. (PMID: 9149941) Ruddy DA … Feder JN (Genome research 1997) 3 4
  5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. (PMID: 32814053) Haenig C … Wanker EE (Cell reports 2020) 3

ExternalLinks

View latest publications for TRIM38 gene in Mastermind

Products for TRIM38 Gene

Sources for TRIM38 Gene