Rnf4 ring finger protein 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rnf4provided by RGD
Official Full Name: ring finger protein 4provided by RGD
Primary source: RGD:3583
See related: EnsemblRapid:ENSRNOG00000013930 AllianceGenome:RGD:3583
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: Enables several functions, including SUMO polymer binding activity; TBP-class protein binding activity; and nuclear receptor binding activity. Involved in several processes, including cellular response to gamma radiation; cellular response to hydroxyurea; and protein ubiquitination. Located in PML body. Orthologous to human RNF4 (ring finger protein 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 362.6), Thymus (RPKM 348.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14q21

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (80625864..80647138, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (76401292..76423270, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (81658400..81679756, complement)

Chromosome 14 - NC_086032.1 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?

Data suggest that ubiquitin-conjugating enzyme E2 variant 2 (Ube2V2) and ring finger protein 4 (RNF4) together induce an active conformation of the ubiquitin-conjugating enzyme Ubc13-ubiquitin (Ubc13~Ub) thioester.
Title: Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains.
crystal structure of the dimeric RING domain of rat RNF4 in complex with E2 (UbcH5A) linked by an isopeptide bond to ubiquitin
Title: Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis.
The dimeric RING ligase RNF4 facilitates ubiquitin transfer by dimeric RING ligases preferentially binding the E2~ubiquitin thioester across the dimer and activating the thioester bond for catalysis.
Title: Mechanism of ubiquitylation by dimeric RING ligase RNF4.
Data show that the RING-domain-containing ubiquitin E3 ligase, RNF4 (also known as SNURF), targets poly-SUMO-modified proteins for degradation mediated by ubiquitin.
Title: RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation.
SNURF is involved in the regulation of processes required for late steps of spermatid maturation
Title: Expression of the nuclear RING finger protein SNURF/RNF4 during rat testis development suggests a role in spermatid maturation.

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 DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables SUMO polymer binding	IDA Inferred from Direct Assay more info	PubMed
enables SUMO polymer binding	IEA Inferred from Electronic Annotation more info
enables SUMO polymer binding	IPI Inferred from Physical Interaction more info	PubMed
enables SUMO polymer binding	ISO Inferred from Sequence Orthology more info
enables TBP-class protein binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables nuclear androgen receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear estrogen receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables nucleosome binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin conjugating enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to arsenic-containing substance	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to cytokine stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to gamma radiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to hydroxyurea	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to testosterone stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in male gonad development	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of protein localization to chromatin	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor 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 proteasome-mediated ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K11-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K48-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K6-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K63-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein autoubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of kinetochore assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of kinetochore assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of kinetochore assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of spindle assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of spindle assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of spindle assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to arsenic-containing substance	IDA Inferred from Direct Assay more info	PubMed
involved_in response to arsenic-containing substance	IEA Inferred from Electronic Annotation more info
involved_in response to arsenic-containing substance	ISO Inferred from Sequence Orthology more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to human chorionic gonadotropin	IEP Inferred from Expression Pattern more info	PubMed
involved_in spermatogenesis	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
colocalizes_with PML body	IBA Inferred from Biological aspect of Ancestor more info
located_in PML body	IDA Inferred from Direct Assay more info	PubMed
located_in PML body	IEA Inferred from Electronic Annotation more info
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in microtubule end	IEA Inferred from Electronic Annotation more info
located_in microtubule end	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF4

Names: E3 ubiquitin ligase RNF4; RING-type E3 ubiquitin transferase RNF4; SNURF; small nuclear ring finger protein

NP_062055.1

EC 2.3.2.27

XP_063129062.1

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_019182.2 → NP_062055.1 E3 ubiquitin-protein ligase RNF4

See identical proteins and their annotated locations for NP_062055.1

Status: PROVISIONAL

Source sequence(s)

BC062024

UniProtKB/Swiss-Prot

O88846

UniProtKB/TrEMBL

A6IK32

Related

ENSRNOP00000096496.1, ENSRNOT00000095762.2

Conserved Domains (1) summary

cd16533
Location:131 → 184

RING-HC_RNF4; RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins