Trim3 tripartite motif-containing 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim3provided by RGD
Official Full Name: tripartite motif-containing 3provided by RGD
Primary source: RGD:70074
See related: EnsemblRapid:ENSRNOG00000018356 AllianceGenome:RGD:70074
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Berp; Rnf22
Summary: Predicted to enable identical protein binding activity and ubiquitin protein ligase activity. Involved in regulation protein catabolic process at postsynapse. Is active in glutamatergic synapse and postsynapse. Orthologous to human TRIM3 (tripartite motif containing 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 183.1), Brain (RPKM 146.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q32

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (169362751..169385430, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (159950921..159973600, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (170441662..170464341, complement)

Chromosome 1 - NC_086019.1 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: 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?

postsynaptic scaffold GKAP is degraded and dendritic spine morphology is regulated by the TRIM3 ubiquitin ligase in rat hippocampal neurons
Title: Degradation of postsynaptic scaffold GKAP and regulation of dendritic spine morphology by the TRIM3 ubiquitin ligase in rat hippocampal neurons.

Submit: New GeneRIF Correction

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 identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology 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 neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of toll-like receptor 3 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of toll-like receptor 3 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein K63-linked ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K63-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in regulation protein catabolic process at postsynapse	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation protein catabolic process at postsynapse	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation protein catabolic process at postsynapse	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
is_active_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in early endosome	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in postsynapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tripartite motif-containing protein 3

Names: brain-expressed RING finger protein; ring finger protein 22; tripartite motif protein 3

NP_113974.2

EC 2.3.2.27

XP_038948510.1

EC 2.3.2.27

XP_038948512.1

EC 2.3.2.27

XP_038948513.1

EC 2.3.2.27

XP_038948514.1

EC 2.3.2.27

XP_063131651.1

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_031786.2 → NP_113974.2 tripartite motif-containing protein 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

O70277

UniProtKB/TrEMBL

A6I7K0, G3V8D6

Related

ENSRNOP00000084221.1, ENSRNOT00000114170.2

Conserved Domains (5) summary

smart00502
Location:158 → 284

BBC; B-Box C-terminal domain

smart00557
Location:322 → 419

IG_FLMN; Filamin-type immunoglobulin domains

cd14960
Location:471 → 744

NHL_TRIM2_like; NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins

cd16768
Location:19 → 63

RING-HC_TRIM3; RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3)

cd19825
Location:107 → 153

Bbox2_TRIM3_C-VII; B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

169362751..169385430 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039092582.2 → XP_038948510.1 tripartite motif-containing protein 3 isoform X1

UniProtKB/Swiss-Prot

O70277

Related

ENSRNOP00000024850.4, ENSRNOT00000024850.7

Conserved Domains (5) summary

smart00502
Location:164 → 290

BBC; B-Box C-terminal domain

smart00557
Location:328 → 425

IG_FLMN; Filamin-type immunoglobulin domains

cd14960
Location:477 → 750

NHL_TRIM2_like; NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins

cd16768
Location:19 → 63

RING-HC_TRIM3; RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3)

cl00034
Location:107 → 159

Bbox_SF; B-box-type zinc finger superfamily
XM_039092584.2 → XP_038948512.1 tripartite motif-containing protein 3 isoform X1

UniProtKB/Swiss-Prot

O70277

Conserved Domains (5) summary

smart00502
Location:164 → 290

BBC; B-Box C-terminal domain

smart00557
Location:328 → 425

IG_FLMN; Filamin-type immunoglobulin domains

cd14960
Location:477 → 750

NHL_TRIM2_like; NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins

cd16768
Location:19 → 63

RING-HC_TRIM3; RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3)

cl00034
Location:107 → 159

Bbox_SF; B-box-type zinc finger superfamily
XM_063275581.1 → XP_063131651.1 tripartite motif-containing protein 3 isoform X2

UniProtKB/Swiss-Prot

O70277

UniProtKB/TrEMBL

A6I7K0, G3V8D6
XM_039092585.2 → XP_038948513.1 tripartite motif-containing protein 3 isoform X1

UniProtKB/Swiss-Prot

O70277

Conserved Domains (5) summary

smart00502
Location:164 → 290

BBC; B-Box C-terminal domain

smart00557
Location:328 → 425

IG_FLMN; Filamin-type immunoglobulin domains

cd14960
Location:477 → 750

NHL_TRIM2_like; NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins

cd16768
Location:19 → 63

RING-HC_TRIM3; RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3)

cl00034
Location:107 → 159

Bbox_SF; B-box-type zinc finger superfamily
XM_039092586.2 → XP_038948514.1 tripartite motif-containing protein 3 isoform X3

UniProtKB/Swiss-Prot

O70277

Conserved Domains (4) summary

smart00502
Location:63 → 189

BBC; B-Box C-terminal domain

smart00557
Location:227 → 324

IG_FLMN; Filamin-type immunoglobulin domains

cd14960
Location:376 → 649

NHL_TRIM2_like; NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins

cl00034
Location:26 → 58

Bbox_SF; B-box-type zinc finger superfamily