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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
  • 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
  • E3 Ubiquitin-Protein Ligase TRIM13 3
  • 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 Chronic Lymphocytic Leukemia and Pain Agnosia. Among its related pathways are Transport to the Golgi and subsequent modification and Calnexin/calreticulin cycle. GO annotations related to this gene include ligase activity and signal transducer activity. An important paralog of this gene is TRIM59.

UniProtKB/Swiss-Prot for TRIM13 Gene

  • E3 ubiquitin 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.

Additional gene information for TRIM13 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRIM13 Gene

Genomics for TRIM13 Gene

Regulatory Elements for TRIM13 Gene

Enhancers for TRIM13 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13H050121 2 FANTOM5 Ensembl ENCODE dbSUPER 34.6 +130.9 130869 10 PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ZNF766 ZNF143 SETDB2 KCNRG TRIM13 CTAGE10P DLEU1 RNASEH2B-AS1 ENSG00000176882 RNASEH2B EBPL DLEU2
GH13H049934 1.3 Ensembl ENCODE 26 -58.1 -58135 5 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 SP3 TRIM13 CTAGE10P KCNRG ENSG00000176882 SETDB2 EBPL DLEU1 GC13P049951 RNY4P9 GC13M049909
GH13H050075 1.4 ENCODE dbSUPER 19 +84.1 84053 9 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 CTAGE10P TRIM13 ENSG00000176882 DLEU1 KCNRG EBPL SETDB2 ENSG00000277752 ENSG00000275559
GH13H049494 1.5 Ensembl ENCODE dbSUPER 12.9 -498.2 -498195 6 HDGF PKNOX1 FOXA2 ARID4B DMAP1 GLI4 ZNF2 YY1 GLIS2 ZNF143 SETDB2 PHF11 TRIM13 KCNRG EBPL ARL11 RCBTB1
GH13H050207 1.5 FANTOM5 Ensembl ENCODE 10 +213.1 213133 2 PKNOX1 ARNT GLI4 GLIS2 ATF7 SMARCA4 GLIS1 NBN HMBOX1 SP7 SETDB2 RPL34P26 RNASEH2B TRIM13 DLEU7 EBPL GC13P050221 GC13P050185
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRIM13 on UCSC Golden Path with GeneCards custom track

Promoters for TRIM13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000062794 1412 2601 ARID4B SIN3A DMAP1 GLI4 ZBTB7B YY1 ZNF121 ZNF766 GLIS2 ELK1

Genomic Location for TRIM13 Gene

Chromosome:
13
Start:
49,995,888 bp from pter
End:
50,020,481 bp from pter
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.
    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

Antibody Products

  • Abcam antibodies for TRIM13

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):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for TRIM13 Gene

GenScript: Design optimal peptide antigens:

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 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.
UniProtKB/Swiss-Prot Function:
E3 ubiquitin 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.

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:0004871 signal transducer activity IMP 12761501
GO:0005515 protein binding IPI 17314412
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with TRIM13: view
genes like me logo Genes that share phenotypes with TRIM13: view

Animal Model Products

CRISPR Products

miRNA for TRIM13 Gene

miRTarBase miRNAs that target TRIM13

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TRIM13
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Animal Models , 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 1
peroxisome 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TRIM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 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.

Interacting Proteins for TRIM13 Gene

Gene Ontology (GO) - Biological Process for TRIM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
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
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, Target, agonist 0
Diprenorphine Illicit, Vet_approved Pharma Full agonist, Agonist, 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

Unigene Clusters for TRIM13 Gene

Tripartite motif containing 13:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TRIM13
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for TRIM13 Gene

GeneLoc Exon Structure for
TRIM13
ECgene alternative splicing isoforms for
TRIM13

Expression for TRIM13 Gene

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

NURSA nuclear receptor signaling pathways regulating expression of TRIM13 Gene:

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)
  • Heart(2.2)
  • Muscle(2.2)
  • Adrenal gland(2.1)
genes like me logo Genes that share expression patterns with TRIM13: view

Primer Products

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 33 34
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia TRIM13 33 34
  • 91.73 (n)
cow
(Bos Taurus)
Mammalia TRIM13 33 34
  • 90.25 (n)
mouse
(Mus musculus)
Mammalia Trim13 33 16 34
  • 86.49 (n)
rat
(Rattus norvegicus)
Mammalia Trim13 33
  • 85.5 (n)
oppossum
(Monodelphis domestica)
Mammalia TRIM13 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRIM13 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRIM13 33 34
  • 72.86 (n)
lizard
(Anolis carolinensis)
Reptilia TRIM13 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492997 33
  • 62.99 (n)
zebrafish
(Danio rerio)
Actinopterygii trim13 33 34
  • 55.73 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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)

Paralogs for TRIM13 Gene

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

Pseudogenes.org Pseudogenes for TRIM13 Gene

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

Variants for TRIM13 Gene

Sequence variations from dbSNP and Humsavar for TRIM13 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs1000276397 -- 50,011,723(+) TGTGT(A/G/T)TAGGA intron-variant
rs1000359371 -- 50,016,196(+) GGTAA(C/T)CAGTG intron-variant, utr-variant-3-prime
rs1000395701 -- 50,004,748(+) GCACT(G/T)CAGTC intron-variant
rs1000719955 -- 50,016,963(+) TTAGC(A/G)ACACA intron-variant, utr-variant-3-prime
rs1000979050 -- 50,003,849(+) TAAAA(A/G)TATGT intron-variant

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)

Relevant External Links 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

(6) MalaCards diseases for TRIM13 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
chronic lymphocytic leukemia
  • b-cell chronic lymphocytic leukemia
pain agnosia
  • analgesia
agnosia
  • dyspraxia
peripheral nervous system neoplasm
  • neoplasm of peripheral nerve
autonomic nervous system neoplasm
  • tumor of autonomic nervous system
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for TRIM13

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 22 60
  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 22 60
  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 22 60
  4. TRIM13 regulates ER stress induced autophagy and clonogenic ability of the cells. (PMID: 22178386) Tomar D … Singh R (Biochimica et biophysica acta 2012) 3 4 60
  5. Ret finger protein 2 enhances ionizing radiation-induced apoptosis via degradation of AKT and MDM2. (PMID: 21333377) Joo HM … Jin YW (European journal of cell biology 2011) 3 4 60

Products for TRIM13 Gene

Sources for TRIM13 Gene

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