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TRIM13 tripartite motif containing 13 [ Homo sapiens (human) ]

Gene ID: 10206, updated on 2-Nov-2024

Summary

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Official Symbol
TRIM13provided by HGNC
Official Full Name
tripartite motif containing 13provided by HGNC
Primary source
HGNC:HGNC:9976
See related
Ensembl:ENSG00000204977 MIM:605661; AllianceGenome:HGNC:9976
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CAR; LEU5; RFP2; DLEU5; RNF77
Summary
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]
Expression
Broad expression in testis (RPKM 17.7), bone marrow (RPKM 8.8) and 25 other tissues See more
Orthologs
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Genomic context

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See TRIM13 in Genome Data Viewer
Location:
13q14.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (49997042..50018467)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (49217709..49239060)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50571178..50592603)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7756 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:50546741-50546933 Neighboring gene Sharpr-MPRA regulatory region 13323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5351 Neighboring gene deleted in lymphocytic leukemia 2 Neighboring gene microRNA 3613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7758 Neighboring gene potassium channel regulator Neighboring gene microRNA 16-1 Neighboring gene microRNA 15a

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Bioinformatics analysis of prognostic value of TRIM13 gene in breast cancer. Chen WX, et al. Biosci Rep, 2019 Mar 29. PMID 30837324, Free PMC Article
  2. 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. Kapanadze B, et al. FEBS Lett, 1998 Apr 17. PMID 9599022
  3. TRIM13 inhibited cell proliferation and induced cell apoptosis by regulating NF-κB pathway in non-small-cell lung carcinoma cells. Xu L, et al. Gene, 2019 Oct 5. PMID 31357025
  4. TRIM13 (RFP2) downregulation decreases tumour cell growth in multiple myeloma through inhibition of NF Kappa B pathway and proteasome activity. Gatt ME, et al. Br J Haematol, 2013 Jul. PMID 23647456, Free PMC Article
  5. RFP2, c13ORF1, and FAM10A4 are the most likely tumor suppressor gene candidates for B-cell chronic lymphocytic leukemia. van Everdink WJ, et al. Cancer Genet Cytogenet, 2003 Oct 1. PMID 14499696

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRIM13 reduces cholesterol efflux and increases oxidized LDL uptake leading to foam cell formation and atherosclerosis.
    Title: TRIM13 reduces cholesterol efflux and increases oxidized LDL uptake leading to foam cell formation and atherosclerosis.
  2. TRIM13 inhibits cell proliferation and induces autophagy in lung adenocarcinoma by regulating KEAP1/NRF2 pathway.
    Title: TRIM13 inhibits cell proliferation and induces autophagy in lung adenocarcinoma by regulating KEAP1/NRF2 pathway.
  3. TRIM3 and TRIM16 as potential tumor suppressors in breast cancer patients.
    Title: TRIM3 and TRIM16 as potential tumor suppressors in breast cancer patients.
  4. Altered DNA methylation of TRIM13 in diabetic nephropathy suppresses mesangial collagen synthesis by promoting ubiquitination of CHOP.
    Title: Altered DNA methylation of TRIM13 in diabetic nephropathy suppresses mesangial collagen synthesis by promoting ubiquitination of CHOP.
  5. Results from bioinformatics analysis suggest that Tripartite motif 13 (TRIM13) may be adopted as a promising predictive biomarker for prognosis of breast cancer.
    Title: Bioinformatics analysis of prognostic value of TRIM13 gene in breast cancer.
  6. The Trim13-mediated ubiquitination of Nur77 was optimal in the presence of the E2 enzyme UbcH5. Importantly, in addition to Trim13-mediated ubiquitination, the stability of Nur77 was also regulated by casein kinase 2alpha
    Title: The E3 ubiquitin ligase Trim13 regulates Nur77 stability via casein kinase 2α.
  7. results indicate that TRIM13 behaves as a tumor suppressor in non-small-cell lung carcinoma through regulating NF-kappaB pathway.
    Title: TRIM13 inhibited cell proliferation and induced cell apoptosis by regulating NF-κB pathway in non-small-cell lung carcinoma cells.
  8. Results from a study on gene expression variability markers in early-stage human embryos shows that TRIM13 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
    Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
  9. TRIM13 mediated NF-kappaB repression is essential for negative regulation of clonogenic ability of the cells.
    Title: TRIM13 regulates ubiquitination and turnover of NEMO to suppress TNF induced NF-κB activation.
  10. Results show that HRD1 and RFP2 contributes are required for the disposal of V247M alpha-sarcoglycan mutant.
    Title: Unveiling the degradative route of the V247M α-sarcoglycan mutant responsible for LGMD-2D.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
  
enables ubiquitin-like protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in ERAD pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ERAD pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in endoplasmic reticulum mannose trimming TAS
Traceable Author Statement
more info
  
involved_in innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of viral transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of canonical NF-kappaB signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of macroautophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of macroautophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein autoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in suppression of viral release by host IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum quality control compartment IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
E3 ubiquitin-protein ligase TRIM13
Names
B-cell chronic lymphocytic leukemia tumor suppressor Leu5
CLL-associated RING finger
RING finger protein 77
RING-type E3 ubiquitin transferase TRIM13
leukemia-associated protein 5
putative tumor suppressor RFP2
ret finger protein 2
tripartite motif protein 13
tripartite motif-containing protein 13
NP_001007279.1
NP_005789.2
NP_434698.1
NP_998755.1

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_001007278.3 → NP_001007279.1  E3 ubiquitin-protein ligase TRIM13 isoform 2

    See identical proteins and their annotated locations for NP_001007279.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an additional internal exon, which contains an upstream in-frame AUG start codon compared to variant 1. The encoded protein (isoform 2) has a longer N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL832695, AY455758, AY764035, KF455768
    Consensus CDS
    CCDS41888.1
    UniProtKB/TrEMBL
    A0A184AP76
    Related
    ENSP00000348299.4, ENST00000356017.8
    Conserved Domains (2) summary
    smart00336
    Location:93 → 134
    BBOX; B-Box-type zinc finger
    cd00162
    Location:12 → 64
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

  2. NM_005798.5 → NP_005789.2  E3 ubiquitin-protein ligase TRIM13 isoform 1

    See identical proteins and their annotated locations for NP_005789.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the same protein (isoform 1) as variants 2 and 3.
    Source sequence(s)
    AF241850, AL832695, AY455758, BI668033, KF455768
    Consensus CDS
    CCDS9423.1
    UniProtKB/Swiss-Prot
    B2RB49, O60858, Q5UBW0, Q5W0U8, Q5W0U9, Q9BQ47, Q9C021
    UniProtKB/TrEMBL
    A0A184AP76
    Related
    ENSP00000412943.2, ENST00000420995.6
    Conserved Domains (3) summary
    smart00336
    Location:90 → 131
    BBOX; B-Box-type zinc finger
    pfam12252
    Location:163 → 234
    SidE; Dot/Icm substrate protein
    cd16762
    Location:5 → 61
    RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins

  3. NM_052811.4 → NP_434698.1  E3 ubiquitin-protein ligase TRIM13 isoform 1

    See identical proteins and their annotated locations for NP_434698.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared variant 1. Variants 1, 2 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AL832695, AY191002, AY455758, BI668033, KF455768
    Consensus CDS
    CCDS9423.1
    UniProtKB/Swiss-Prot
    B2RB49, O60858, Q5UBW0, Q5W0U8, Q5W0U9, Q9BQ47, Q9C021
    UniProtKB/TrEMBL
    A0A184AP76
    Related
    ENSP00000399206.2, ENST00000457662.2
    Conserved Domains (3) summary
    smart00336
    Location:90 → 131
    BBOX; B-Box-type zinc finger
    pfam12252
    Location:163 → 234
    SidE; Dot/Icm substrate protein
    cd16762
    Location:5 → 61
    RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins

  4. NM_213590.3 → NP_998755.1  E3 ubiquitin-protein ligase TRIM13 isoform 1

    See identical proteins and their annotated locations for NP_998755.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AL832695, AY455758, KF455768
    Consensus CDS
    CCDS9423.1
    UniProtKB/Swiss-Prot
    B2RB49, O60858, Q5UBW0, Q5W0U8, Q5W0U9, Q9BQ47, Q9C021
    UniProtKB/TrEMBL
    A0A184AP76
    Related
    ENSP00000367424.3, ENST00000378182.4
    Conserved Domains (3) summary
    smart00336
    Location:90 → 131
    BBOX; B-Box-type zinc finger
    pfam12252
    Location:163 → 234
    SidE; Dot/Icm substrate protein
    cd16762
    Location:5 → 61
    RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    49997042..50018467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    49217709..49239060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60858.2 GenPept UniProtKB/Swiss-Prot:O60858

Gene LinkOut

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