Trim13 tripartite motif-containing 13 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim13provided by RGD
Official Full Name: tripartite motif-containing 13provided by RGD
Primary source: RGD:1307609
See related: EnsemblRapid:ENSRNOG00000009075 AllianceGenome:RGD:1307609
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable transcription coactivator activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including defense response to symbiont; negative regulation of viral transcription; and proteasomal protein catabolic process. Predicted to be located in endoplasmic reticulum membrane and perinuclear endoplasmic reticulum. Predicted to be active in cytoplasm. Orthologous to human TRIM13 (tripartite motif containing 13). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 81.5), Brain (RPKM 38.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p12

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (39909587..39948719)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (35733548..35772676)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (41897191..41936545)

Chromosome 15 - NC_086033.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables transcription coactivator activity	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-like protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-like protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in ERAD pathway	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of viral transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of viral transcription	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of macroautophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of macroautophagy	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in protein autoubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in suppression of viral release by host	IEA Inferred from Electronic Annotation more info
involved_in suppression of viral release by host	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in perinuclear endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in perinuclear endoplasmic reticulum	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM13

Names: RING-type E3 ubiquitin transferase TRIM13; putative tumor suppressor RFP2; ret finger protein 2; tripartite motif protein 13; tripartite motif-containing protein 13

NP_001012210.1

EC 2.3.2.27

XP_063130551.1

EC 2.3.2.27

XP_063130552.1

EC 2.3.2.27

XP_063130553.1

EC 2.3.2.27

XP_063130554.1

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_001012210.1 → NP_001012210.1 E3 ubiquitin-protein ligase TRIM13

See identical proteins and their annotated locations for NP_001012210.1

Status: PROVISIONAL

Source sequence(s)

BC088425

UniProtKB/Swiss-Prot

Q5M7V1

Related

ENSRNOP00000099165.1, ENSRNOT00000167033.1

Conserved Domains (2) summary

cd16762
Location:5 → 61

RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins

cd19767
Location:92 → 133

Bbox2_TRIM13_C-XI; B-box-type 2 zinc finger found in tripartite motif-containing protein 13 (TRIM13) and similar proteins