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

Summary

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: mouse all
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Genomic context

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_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
TRIM3 and TRIM16 as potential tumor suppressors in breast cancer patients.
Title: TRIM3 and TRIM16 as potential tumor suppressors in breast cancer patients.
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.
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.
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.
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.
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.
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.
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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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10S275 (e-PCR)
- UniSTS:147992

RH94230 (e-PCR)
- UniSTS:92497

D13S1476 (e-PCR)
- UniSTS:154735

D1S1423 (e-PCR)
- UniSTS:149619

G35510 (e-PCR)
- UniSTS:44150

RH45034 (e-PCR)
- UniSTS:18641

TRIM13 (e-PCR)
- UniSTS:505317

D11S3316 (e-PCR)
- UniSTS:152558

RH44787 (e-PCR)
- UniSTS:6904

WI-10171 (e-PCR)
- UniSTS:83448

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 more info	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

EC 2.3.2.27

NP_005789.2

EC 2.3.2.27

NP_434698.1

EC 2.3.2.27

NP_998755.1

EC 2.3.2.27

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)

NM_001007278.3 → NP_001007279.1 E3 ubiquitin-protein ligase TRIM13 isoform 2

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

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
NM_052811.4 → NP_434698.1 E3 ubiquitin-protein ligase TRIM13 isoform 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
NM_213590.3 → NP_998755.1 E3 ubiquitin-protein ligase TRIM13 isoform 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