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Aliases for TRIM38 Gene

Aliases for TRIM38 Gene

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

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. 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 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 , fRNAdb sequence ontologies and piRNA Summary for TRIM38 Gene

Genomics for TRIM38 Gene

GeneHancer (GH) Regulatory Elements for TRIM38 Gene

Promoters and enhancers for TRIM38 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J025958 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 661.5 -0.8 -767 6.5 HDGF PKNOX1 SMAD1 ARID4B FEZF1 IRF4 YY1 POLR2B ZNF207 SP3 TRIM38 ENSG00000272462 ABT1 NUP50P2 HMGN4 BTN2A3P BTN3A2 BTN2A1 SLC17A4 SLC17A2
GH06J026382 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 19.7 +420.7 420678 2.2 HDGF PKNOX1 FOXA2 ARNT FEZF1 YBX1 ZNF2 YY1 POLR2B E2F8 BTN2A2 ABT1 BTN2A1 HMGN4 BTN2A3P BTN3A1 TRIM38 GUSBP2 BTN3A2 ZNF391
GH06J026341 Enhancer 1.5 Ensembl ENCODE dbSUPER 19.7 +379.5 379501 1.6 MLX YBX1 ZNF213 E2F8 ZNF143 ZNF548 ZNF263 SP3 NFYC MEF2D ABT1 BTN2A3P HMGN4 BTN2A2 BTN2A1 ZNF322 BTN3A2 TRIM38 HIST1H2APS4 ENSG00000271071
GH06J026534 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 11.1 +574.4 574385 5 MLX FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D HMGN4 PIR54163 TRV-CAC1-6 TRR-ACG1-2 LOC102724851 ABT1 BTN3A2 BTN2A1 ZNF322 BTN2A3P
GH06J026019 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.1 +64.9 64897 16.2 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 HIST1H4B HIST1H3B HIST1H2AB ABT1 BTN2A1 BTN2A3P HMGN4 BTN2A2 ENSG00000272462 BTN3A2
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for TRIM38 Gene

Genomic Locations for TRIM38 Gene
chr6:25,962,689-25,991,226
(GRCh38/hg38)
Size:
28,538 bases
Orientation:
Plus strand
chr6:25,963,030-25,987,384
(GRCh37/hg19)
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 StructureGene Density

RefSeq DNA sequence for TRIM38 Gene

Proteins for TRIM38 Gene

  • 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

Post-translational modifications for TRIM38 Gene

  • Ubiquitination at isoforms=227, isoforms=137, and isoforms=122
  • Modification sites at PhosphoSitePlus

Other Protein References for TRIM38 Gene

No data available for DME Specific Peptides for TRIM38 Gene

Domains & Families for TRIM38 Gene

Gene Families for TRIM38 Gene

Suggested Antigen Peptide Sequences for TRIM38 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

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

Function for TRIM38 Gene

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:
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.

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:0004871 obsolete signal transducer activity HMP --
GO:0005515 protein binding IPI 11854271
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
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 Model Products

Clone Products

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
cytosol 5
nucleus 3
plasma membrane 2
cytoskeleton 2

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:0005622 intracellular IEA --
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:0016567 protein ubiquitination IEA --
GO:0032648 regulation of interferon-beta production IEA --
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling IDA 23077300
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IEA --
GO:0045070 positive regulation of viral genome replication IEA --
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

No Compound Related Data Available

Transcripts for TRIM38 Gene

mRNA/cDNA for TRIM38 Gene

Unigene Clusters for TRIM38 Gene

Tripartite motif containing 38:
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
TRIM38

Expression for TRIM38 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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

NURSA nuclear receptor signaling pathways regulating expression of TRIM38 Gene:

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(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with TRIM38: view

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 34 33
  • 99.14 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TRIM38 34 33
  • 84.24 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TRIM38 34 33
  • 81.15 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Trim38 16 34 33
  • 69.86 (n)
rat
(Rattus norvegicus)
Mammalia LOC680019 33
  • 64.04 (n)
chicken
(Gallus gallus)
Aves -- 34
  • 35 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 35 (a)
OneToMany
Species where no ortholog for TRIM38 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

Pseudogenes.org Pseudogenes for TRIM38 Gene

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

Variants for TRIM38 Gene

Sequence variations from dbSNP and Humsavar for TRIM38 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000074104 -- 25,975,760(+) T/C intron_variant, non_coding_transcript_variant
rs1000334942 -- 25,969,727(+) T/G intron_variant
rs1000386608 -- 25,976,118(+) G/A intron_variant, non_coding_transcript_variant
rs1000449235 -- 25,969,247(+) T/C intron_variant
rs1000479702 -- 25,962,678(+) G/A upstream_transcript_variant

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

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

Disorders for TRIM38 Gene

Additional Disease Information for TRIM38

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TRIM38 Gene.

No data available for MalaCards , 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 58
  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 44 58
  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 58
  4. A 1.1-Mb transcript map of the hereditary hemochromatosis locus. (PMID: 9149941) Ruddy DA … Feder JN (Genome research 1997) 3 4 58
  5. NLRP6 facilitates the interaction between TAB2/3 and TRIM38 in rheumatoid arthritis fibroblast-like synoviocytes. (PMID: 28295271) Lin Y … Luo Z (FEBS letters 2017) 3 58

Products for TRIM38 Gene

Sources for TRIM38 Gene

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