Trim39 tripartite motif-containing 39 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim39provided by RGD
Official Full Name: tripartite motif-containing 39provided by RGD
Primary source: RGD:1303115
See related: EnsemblRapid:ENSRNOG00000000785 AllianceGenome:RGD:1303115
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: Rnf23
Summary: Predicted to enable identical protein binding activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle phase transition; and regulation of signal transduction. Predicted to be located in mitochondrion and nucleus. Predicted to be active in cytosol. Orthologous to human TRIM39 (tripartite motif containing 39). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 106.4), Spleen (RPKM 68.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (2008528..2022383)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (2003320..2017175)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (2500691..2514546)

Chromosome 20 - NC_086038.1 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
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?

Submit: New GeneRIF Correction

General gene information

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Markers

BF415953 (e-PCR)
- UniSTS:248973

RH137959 (e-PCR)
- UniSTS:220046

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 ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic G2 DNA damage checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in mitotic G2 DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in mitotic G2 DNA damage checkpoint signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in phosphorelay signal transduction system	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein stabilization	IEA Inferred from Electronic Annotation more info
involved_in protein stabilization	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle G1/S phase transition	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle G1/S phase transition	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle G1/S phase transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

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

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM39

Names: RING finger protein 23; RING-type E3 ubiquitin transferase TRIM39; tripartite motif protein 39; tripartite motif-containing protein 39

NP_998727.1

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_213562.1 → NP_998727.1 E3 ubiquitin-protein ligase TRIM39

See identical proteins and their annotated locations for NP_998727.1

Status: VALIDATED

Source sequence(s)

BX883050

UniProtKB/Swiss-Prot

Q6MFZ5

UniProtKB/TrEMBL

A0A8L2PYM6, A6KR95

Related

ENSRNOP00000098163.2, ENSRNOT00000120505.2

Conserved Domains (4) summary

PRK02224
Location:144 → 271

PRK02224; DNA double-strand break repair Rad50 ATPase

cd13745
Location:305 → 483

SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like

cd16601
Location:26 → 69

RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins

cd19780
Location:103 → 146

Bbox2_TRIM39-like; B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins