Trim21 tripartite motif-containing 21 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim21provided by RGD
Official Full Name: tripartite motif-containing 21provided by RGD
Primary source: RGD:1305795
See related: Ensembl:ENSRNOG00000018517 AllianceGenome:RGD:1305795
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
Summary: Predicted to enable several functions, including protein homodimerization activity; transcription coactivator activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including defense response to other organism; protein ubiquitination; and regulation of DNA-binding transcription factor activity. Predicted to be located in nucleus. Predicted to be part of SCF ubiquitin ligase complex. Predicted to be active in cytosol and nucleoplasm. Orthologous to human TRIM21 (tripartite motif containing 21). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 149.6), Lung (RPKM 142.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q32

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (166376829..166399441, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (156964896..156987504, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (167686148..167708735, 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?

Cx43/TRIM21 complex is an active participant of gap junction ubiquitylation and turnover.
Title: Association of connexin43 with E3 ubiquitin ligase TRIM21 reveals a mechanism for gap junction phosphodegron control.
suppression of TRIM21 resulting from altered NF-kappaB and IRF homeostasis accelerates the ONFH in rats treated with corticosteroids following LPS administration
Title: The suppression of TRIM21 and the accumulation of IFN-α play crucial roles in the pathogenesis of osteonecrosis of the femoral head.

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	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein kinase binding	IBA Inferred from Biological aspect of Ancestor 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 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 innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein deubiquitination	ISO Inferred from Sequence Orthology 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	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of autophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of autophagy	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 cell cycle	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in proteasomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in protein K27-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K48-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K6-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K63-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein monoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein polyubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in pyroptosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of viral entry into host cell	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to type II interferon	ISO Inferred from Sequence Orthology more info
involved_in stress granule disassembly	ISO Inferred from Sequence Orthology more info
involved_in suppression of viral release by host	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SCF ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasmic stress granule	ISO Inferred from Sequence Orthology more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM21

Names: 52 kDa Ro protein; tripartite motif protein 21

NP_001076041.1

EC 2.3.2.27

XP_006229946.1

EC 2.3.2.27

XP_038934047.1

EC 2.3.2.27

XP_038934048.1

EC 2.3.2.27

XP_038934055.1

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_001082572.2 → NP_001076041.1 E3 ubiquitin-protein ligase TRIM21

See identical proteins and their annotated locations for NP_001076041.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A6I748

Conserved Domains (4) summary

smart00336
Location:92 → 132

BBOX; B-Box-type zinc finger

cd00162
Location:19 → 62

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 ...

pfam13094
Location:188 → 270

CENP-Q; CENP-Q, a CENPA-CAD centromere complex subunit

cd12900
Location:291 → 469

SPRY_PRY_TRIM21; PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52)

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

166376829..166399441 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039078119.1 → XP_038934047.1 E3 ubiquitin-protein ligase TRIM21 isoform X2

Conserved Domains (5) summary

TIGR00570
Location:16 → 205

cdk7; CDK-activating kinase assembly factor MAT1

cd12900
Location:259 → 437

SPRY_PRY_TRIM21; PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52)

cd00162
Location:20 → 58

RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]

cd19772
Location:96 → 133

Bbox2_TRIM21_C-IV; B-box-type 2 zinc finger found in tripartite motif-containing protein 21 (TRIM21) and similar proteins

cl17238
Location:16 → 59

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
XM_006229884.3 → XP_006229946.1 E3 ubiquitin-protein ligase TRIM21 isoform X1

UniProtKB/TrEMBL

D4ACF2

Related

ENSRNOP00000024992.6, ENSRNOT00000024992.7

Conserved Domains (4) summary

smart00336
Location:92 → 132

BBOX; B-Box-type zinc finger

cd00162
Location:19 → 62

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 ...

pfam13094
Location:197 → 279

CENP-Q; CENP-Q, a CENPA-CAD centromere complex subunit

cd12900
Location:300 → 478

SPRY_PRY_TRIM21; PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52)
XM_039078120.2 → XP_038934048.1 E3 ubiquitin-protein ligase TRIM21 isoform X3

Conserved Domains (2) summary

cd12900
Location:139 → 317

SPRY_PRY_TRIM21; PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52)

pfam02841
Location:26 → 98

GBP_C; Guanylate-binding protein, C-terminal domain
XM_039078127.2 → XP_038934055.1 E3 ubiquitin-protein ligase TRIM21 isoform X4

Conserved Domains (2) summary

cd12900
Location:130 → 308

SPRY_PRY_TRIM21; PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52)

pfam02841
Location:17 → 89

GBP_C; Guanylate-binding protein, C-terminal domain