This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This gene is located on chromosome 13 within the minimal deletion region for B-cell chronic lymphocytic leukemia. Multiple alternatively spliced transcript variants have been found for this gen... See more...

Aliases for TRIM13 Gene

Aliases for TRIM13 Gene

  • Tripartite Motif Containing 13 2 3 5
  • Ret Finger Protein 2 2 3 4
  • B-Cell Chronic Lymphocytic Leukemia Tumor Suppressor Leu5 3 4
  • RING-Type E3 Ubiquitin Transferase TRIM13 3 4
  • Tripartite Motif-Containing Protein 13 3 4
  • E3 Ubiquitin-Protein Ligase TRIM13 3 4
  • Putative Tumor Suppressor RFP2 3 4
  • Leukemia-Associated Protein 5 3 4
  • RING Finger Protein 77 3 4
  • RNF77 3 4
  • RFP2 3 4
  • LEU5 3 4
  • Tripartite Motif-Containing 13 2
  • Tripartite Motif Protein 13 3
  • CLL-Associated RING Finger 3
  • EC 2.3.2.27 4
  • DLEU5 3
  • CAR 3

External Ids for TRIM13 Gene

Previous HGNC Symbols for TRIM13 Gene

  • RFP2

Previous GeneCards Identifiers for TRIM13 Gene

  • GC13P049472
  • GC13P050570
  • GC13P031366

Summaries for TRIM13 Gene

Entrez Gene Summary for TRIM13 Gene

  • This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This gene is located on chromosome 13 within the minimal deletion region for B-cell chronic lymphocytic leukemia. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for TRIM13 Gene

TRIM13 (Tripartite Motif Containing 13) is a Protein Coding gene. Diseases associated with TRIM13 include Lymphocytic Leukemia and Immune Defect Due To Absence Of Thymus. Among its related pathways are Metabolism of proteins and Calnexin/calreticulin cycle. Gene Ontology (GO) annotations related to this gene include ligase activity and obsolete signal transducer activity. An important paralog of this gene is TRIM69.

UniProtKB/Swiss-Prot Summary for TRIM13 Gene

  • Endoplasmic reticulum (ER) membrane anchored E3 ligase involved in the retrotranslocation and turnover of membrane and secretory proteins from the ER through a set of processes named ER-associated degradation (ERAD). This process acts on misfolded proteins as well as in the regulated degradation of correctly folded proteins. Enhances ionizing radiation-induced p53/TP53 stability and apoptosis via ubiquitinating MDM2 and AKT1 and decreasing AKT1 kinase activity through MDM2 and AKT1 proteasomal degradation. Regulates ER stress-induced autophagy, and may act as a tumor suppressor (PubMed:22178386). Plays also a role in innate immune response by stimulating NF-kappa-B activity in the TLR2 signaling pathway. Ubiquitinates TRAF6 via the 'Lys-29'-linked polyubiquitination chain resulting in NF-kappa-B activation (PubMed:28087809). Participates as well in T-cell receptor-mediated NF-kappa-B activation (PubMed:25088585). In the presence of TNF, modulates the IKK complex by regulating IKBKG/NEMO ubiquitination leading to the repression of NF-kappa-B (PubMed:25152375).

Additional gene information for TRIM13 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRIM13 Gene

Genomics for TRIM13 Gene

GeneHancer (GH) Regulatory Elements for TRIM13 Gene

Promoters and enhancers for TRIM13 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 TRIM13 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRIM13

Top Transcription factor binding sites by QIAGEN in the TRIM13 gene promoter:
  • aMEF-2
  • Cart-1
  • HOXA5
  • HSF1 (long)
  • HSF1short
  • MEF-2A
  • POU2F1
  • POU2F1a
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for TRIM13 Gene

Genomic Locations for TRIM13 Gene
chr13:49,995,888-50,020,481
(GRCh38/hg38)
Size:
24,594 bases
Orientation:
Plus strand
chr13:50,570,024-50,594,617
(GRCh37/hg19)
Size:
24,594 bases
Orientation:
Plus strand

Genomic View for TRIM13 Gene

Genes around TRIM13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRIM13 Gene

Proteins for TRIM13 Gene

  • Protein details for TRIM13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60858-TRI13_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase TRIM13
    Protein Accession:
    O60858
    Secondary Accessions:
    • B2RB49
    • Q5UBW0
    • Q5W0U8
    • Q5W0U9
    • Q9BQ47
    • Q9C021

    Protein attributes for TRIM13 Gene

    Size:
    407 amino acids
    Molecular mass:
    46988 Da
    Quaternary structure:
    • Interacts (via C-terminal domain) with VCP. Interacts with AKT1; the interaction ubiquitinates AKT1 and leads to its proteasomal degradation. Interacts with MDM2; the interaction ubiquitinates AKT1 and leads to its proteasomal degradation. Interacts with p62/SQSTM1. Interacts with TRAF6 (PubMed:28087809). Interacts with IKBKG/NEMO (PubMed:25152375).
    Miscellaneous:
    • Located on chromosome 13 within the minimal deletion region for B-cell chronic lymphocytic leukemia.

    Alternative splice isoforms for TRIM13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM13 Gene

Post-translational modifications for TRIM13 Gene

  • Auto-ubiquitinated; requires the RING-type zinc finger. Auto-polyubiquitination leads to proteasomal degradation.
  • Ubiquitination at Lys125
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TRIM13 Gene

Domains & Families for TRIM13 Gene

Gene Families for TRIM13 Gene

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

Protein Domains for TRIM13 Gene

Blocks:
  • Zn-finger, RING
  • B-box zinc finger signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TRIM13 Gene

GenScript: Design optimal peptide antigens:
  • Tripartite motif-containing protein 13 (TRI13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O60858

UniProtKB/Swiss-Prot:

TRI13_HUMAN :
  • The coiled-coil domain is required for the induction of autophagy during endoplasmic reticulum (ER) stress.
  • Belongs to the TRIM/RBCC family.
Domain:
  • The coiled-coil domain is required for the induction of autophagy during endoplasmic reticulum (ER) stress.
  • The RING-type zinc finger is required for auto-polyubiquitination.
  • The C-terminal domain transmembrane domain is indispensable for the localization to the ER.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM13: view

Function for TRIM13 Gene

Molecular function for TRIM13 Gene

UniProtKB/Swiss-Prot Function:
Endoplasmic reticulum (ER) membrane anchored E3 ligase involved in the retrotranslocation and turnover of membrane and secretory proteins from the ER through a set of processes named ER-associated degradation (ERAD). This process acts on misfolded proteins as well as in the regulated degradation of correctly folded proteins. Enhances ionizing radiation-induced p53/TP53 stability and apoptosis via ubiquitinating MDM2 and AKT1 and decreasing AKT1 kinase activity through MDM2 and AKT1 proteasomal degradation. Regulates ER stress-induced autophagy, and may act as a tumor suppressor (PubMed:22178386). Plays also a role in innate immune response by stimulating NF-kappa-B activity in the TLR2 signaling pathway. Ubiquitinates TRAF6 via the 'Lys-29'-linked polyubiquitination chain resulting in NF-kappa-B activation (PubMed:28087809). Participates as well in T-cell receptor-mediated NF-kappa-B activation (PubMed:25088585). In the presence of TNF, modulates the IKK complex by regulating IKBKG/NEMO ubiquitination leading to the repression of NF-kappa-B (PubMed:25152375).
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 TRIM13 Gene

Phenotypes From GWAS Catalog for TRIM13 Gene

Gene Ontology (GO) - Molecular Function for TRIM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IDA 17314412
GO:0005515 protein binding IPI 17314412
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 TRIM13: view
genes like me logo Genes that share phenotypes with TRIM13: view

Animal Models for TRIM13 Gene

MGI Knock Outs for TRIM13:

Animal Model Products

CRISPR Products

miRNA for TRIM13 Gene

miRTarBase miRNAs that target TRIM13

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRIM13 Gene

Localization for TRIM13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM13 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein. Note=Concentrates and colocalizes with p62/SQSTM1 and ZFYVE1 at the perinuclear endoplasmic reticulum.

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 TRIM13 gene
Compartment Confidence
endoplasmic reticulum 5
nucleus 3
plasma membrane 2
mitochondrion 2
cytosol 2
extracellular 1
cytoskeleton 1
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TRIM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TRIM13: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TRIM13 Gene

Pathways & Interactions for TRIM13 Gene

genes like me logo Genes that share pathways with TRIM13: view

UniProtKB/Swiss-Prot O60858-TRI13_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for TRIM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009653 anatomical structure morphogenesis TAS 9599022
GO:0010332 response to gamma radiation IEP 21333377
GO:0010942 positive regulation of cell death IDA 21333377
GO:0016239 positive regulation of macroautophagy IDA 22178386
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with TRIM13: view

No data available for SIGNOR curated interactions for TRIM13 Gene

Drugs & Compounds for TRIM13 Gene

(4) Drugs for TRIM13 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
dihydromorphine Experimental, Illicit Pharma Full agonist, Agonist, Partial agonist, Target, agonist 0
Diprenorphine Illicit, Vet_approved Pharma Full agonist, Agonist, Antagonist, Target 4
Etorphine Illicit, Vet_approved Pharma Full agonist, Agonist, Target, agonist 0
genes like me logo Genes that share compounds with TRIM13: view

Transcripts for TRIM13 Gene

mRNA/cDNA for TRIM13 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM13 Gene

No ASD Table

Relevant External Links for TRIM13 Gene

GeneLoc Exon Structure for
TRIM13

Expression for TRIM13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRIM13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRIM13 Gene

This gene is overexpressed in Bone (48.6) and Peripheral blood mononuclear cells (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRIM13 Gene



Protein tissue co-expression partners for TRIM13 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRIM13

SOURCE GeneReport for Unigene cluster for TRIM13 Gene:

Hs.436922

Evidence on tissue expression from TISSUES for TRIM13 Gene

  • Nervous system(4.9)
  • Blood(4.4)
  • Lung(4.2)
  • Intestine(2.6)
  • Muscle(2.2)
  • Adrenal gland(2.1)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with TRIM13: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM13 Gene

Orthologs for TRIM13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRIM13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRIM13 31 30
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TRIM13 31 30
  • 91.73 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TRIM13 31 30
  • 90.25 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Trim13 17 31 30
  • 86.49 (n)
rat
(Rattus norvegicus)
Mammalia Trim13 30
  • 85.5 (n)
oppossum
(Monodelphis domestica)
Mammalia TRIM13 31
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRIM13 31
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRIM13 31 30
  • 72.86 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TRIM13 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492997 30
  • 62.99 (n)
zebrafish
(Danio rerio)
Actinopterygii trim13 31 30
  • 55.73 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 21 (a)
OneToMany
Species where no ortholog for TRIM13 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TRIM13 Gene

ENSEMBL:
Gene Tree for TRIM13 (if available)
TreeFam:
Gene Tree for TRIM13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRIM13: view image

Paralogs for TRIM13 Gene

(3) SIMAP similar genes for TRIM13 Gene using alignment to 2 proteins:

  • TRI13_HUMAN
  • L8E9D0_HUMAN

Pseudogenes.org Pseudogenes for TRIM13 Gene

genes like me logo Genes that share paralogs with TRIM13: view

Variants for TRIM13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRIM13 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs1056543 - p.Ser355Thr

Additional dbSNP identifiers (rs#s) for TRIM13 Gene

Structural Variations from Database of Genomic Variants (DGV) for TRIM13 Gene

Variant ID Type Subtype PubMed ID
esv2661834 CNV deletion 23128226
esv2747402 CNV deletion 23290073
esv3580637 CNV loss 25503493
esv3632062 CNV loss 21293372
nsv1035151 CNV loss 25217958
nsv1118263 CNV deletion 24896259
nsv472293 CNV novel sequence insertion 20440878
nsv561618 CNV loss 21841781

Variation tolerance for TRIM13 Gene

Residual Variation Intolerance Score: 31.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRIM13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM13 Gene

Disorders for TRIM13 Gene

MalaCards: The human disease database

(7) MalaCards diseases for TRIM13 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
lymphocytic leukemia
  • lymphoblastic leukemia
immune defect due to absence of thymus
  • t-lymphocyte deficiency
leukemia
  • leukemias
adrenal gland pheochromocytoma
  • pheochromocytoma
late-onset retinal degeneration
  • retinitis pigmentosa
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRIM13

genes like me logo Genes that share disorders with TRIM13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRIM13 Gene

Publications for TRIM13 Gene

  1. A cosmid and cDNA fine physical map of a human chromosome 13q14 region frequently lost in B-cell chronic lymphocytic leukemia and identification of a new putative tumor suppressor gene, Leu5. (PMID: 9599022) Kapanadze B … Yankovsky N (FEBS letters 1998) 2 3 4 23 54
  2. The RBCC gene RFP2 (Leu5) encodes a novel transmembrane E3 ubiquitin ligase involved in ERAD. (PMID: 17314412) Lerner M … Sangfelt O (Molecular biology of the cell 2007) 3 4 23 54
  3. Nucleotide sequence, transcription map, and mutation analysis of the 13q14 chromosomal region deleted in B-cell chronic lymphocytic leukemia. (PMID: 11264177) Migliazza A … Dalla-Favera R (Blood 2001) 3 4 23 54
  4. Trim13 Potentiates Toll-Like Receptor 2-Mediated Nuclear Factor κB Activation via K29-Linked Polyubiquitination of Tumor Necrosis Factor Receptor-Associated Factor 6. (PMID: 28087809) Huang B … Baek SH (Molecular pharmacology 2017) 3 4 54
  5. TRIM13 regulates ubiquitination and turnover of NEMO to suppress TNF induced NF-κB activation. (PMID: 25152375) Tomar D … Singh R (Cellular signalling 2014) 3 4 54

Products for TRIM13 Gene

Sources for TRIM13 Gene