Trim23 tripartite motif-containing 23 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim23provided by RGD
Official Full Name: tripartite motif-containing 23provided by RGD
Primary source: RGD:621587
See related: EnsemblRapid:ENSRNOG00000012354 AllianceGenome:RGD:621587
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: Ard1; Arfd1
Summary: Enables GTP binding activity. Involved in positive regulation of protein modification process. Predicted to be located in Golgi membrane and nucleus. Predicted to be active in lysosomal membrane and plasma membrane. Orthologous to human TRIM23 (tripartite motif containing 23). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 246.9), Muscle (RPKM 169.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q13

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (37036193..37069024)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (35302405..35335746)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (34255300..34288140)

Chromosome 2 - NC_086020.1 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 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?

Integrated analysis and validation of TRIM23/p53 signaling pathway in hepatic stellate cells ferroptosis and liver fibrosis.
Title: Integrated analysis and validation of TRIM23/p53 signaling pathway in hepatic stellate cells ferroptosis and liver fibrosis.
Epidermal growth factor receptor-extracellular-regulated kinase blockade upregulates TRIM32 signaling cascade and promotes neurogenesis after spinal cord injury.
Title: Epidermal growth factor receptor-extracellular-regulated kinase blockade upregulates TRIM32 signaling cascade and promotes neurogenesis after spinal cord injury.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH129699 (e-PCR)
- UniSTS:212995

RH144040 (e-PCR)
- UniSTS:233286

MARC_15693-15694:1017691889:1 (e-PCR)
- UniSTS:267869

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables GDP binding	IEA Inferred from Electronic Annotation more info
enables GDP binding	ISO Inferred from Sequence Orthology more info
enables GDP binding	ISS Inferred from Sequence or Structural Similarity more info
enables GTP binding	IBA Inferred from Biological aspect of Ancestor more info
enables GTP binding	IDA Inferred from Direct Assay more info	PubMed
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTP binding	ISO Inferred from Sequence Orthology more info
enables GTP binding	ISS Inferred from Sequence or Structural Similarity more info
enables GTPase activity	IEA Inferred from Electronic Annotation more info
enables GTPase activity	ISO Inferred from Sequence Orthology more info
enables GTPase activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables transferase activity	IEA Inferred from Electronic Annotation 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 ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of autophagy	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein modification process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in Golgi membrane	ISO Inferred from Sequence Orthology more info
located_in Golgi membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM23

Names: ADP-ribosylation factor domain protein 1, 64kD; ADP-ribosylation factor domain-containing protein 1; GTP-binding protein ARD-1; RING-type E3 ubiquitin transferase TRIM23; nucleotide binding protein; tripartite motif protein 23; tripartite motif-containing protein 23

NP_001094107.1

EC 2.3.2.27

XP_008758905.1

EC 2.3.2.27

XP_008758906.1

EC 2.3.2.27

XP_063138685.1

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_001100637.1 → NP_001094107.1 E3 ubiquitin-protein ligase TRIM23

Status: VALIDATED

Source sequence(s)

AA965268, CB696360, CK470479, DV726798, FM052834, FM085917, L04760

UniProtKB/Swiss-Prot

D3ZT39, P36407

Related

ENSRNOP00000102803.1, ENSRNOT00000131125.1

Conserved Domains (6) summary

smart00336
Location:173 → 219

BBOX; B-Box-type zinc finger

cd04158
Location:406 → 574

ARD1; (ADP-ribosylation factor domain protein 1 (ARD1)

cd00021
Location:125 → 168

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

pfam00071
Location:406 → 565

Ras; Ras family

pfam13445
Location:31 → 73

zf-RING_UBOX; RING-type zinc-finger

cl23765
Location:226 → 370

iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

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_086020.1 Reference GRCr8

Range

37036193..37069024

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063282615.1 → XP_063138685.1 E3 ubiquitin-protein ligase TRIM23 isoform X3
XM_008760684.4 → XP_008758906.1 E3 ubiquitin-protein ligase TRIM23 isoform X2

UniProtKB/Swiss-Prot

D3ZT39, P36407

Conserved Domains (5) summary

smart00502
Location:220 → 364

BBC; B-Box C-terminal domain

cd04158
Location:400 → 568

ARD1; (ADP-ribosylation factor domain protein 1 (ARD1)

smart00184
Location:58 → 101

RING; Ring finger

cd00021
Location:152 → 195

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

pfam00071
Location:400 → 559

Ras; Ras family
XM_008760683.4 → XP_008758905.1 E3 ubiquitin-protein ligase TRIM23 isoform X1

UniProtKB/Swiss-Prot

D3ZT39, P36407

UniProtKB/TrEMBL

F1LSC5

Related

ENSRNOP00000016647.5, ENSRNOT00000016649.8

Conserved Domains (6) summary

smart00502
Location:253 → 397

BBC; B-Box C-terminal domain

smart00336
Location:200 → 246

BBOX; B-Box-type zinc finger

cd04158
Location:433 → 601

ARD1; (ADP-ribosylation factor domain protein 1 (ARD1)

cd00021
Location:152 → 195

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

pfam00071
Location:433 → 592

Ras; Ras family

pfam13445
Location:58 → 100

zf-RING_UBOX; RING-type zinc-finger