Rnf5 ring finger protein 5 [Rattus norvegicus (Norway rat)] - Gene - NCBI

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Rnf5 ring finger protein 5 [ Rattus norvegicus (Norway rat) ]
Gene ID: 407784, updated on 9-Dec-2024

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Gene Sequences (FASTA)

Transcript sequences (FASTA)

Protein sequences(FASTA)

In addition, your package will include a detailed data report in both TSV and JSONL formats.

File name
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Summary

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Official Symbol

Rnf5provided by RGD

Official Full Name

ring finger protein 5provided by RGD

Primary source

RGD:1588458

See related

EnsemblRapid:ENSRNOG00000000438 AllianceGenome:RGD:1588458

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 identical protein binding activity; ubiquitin protein ligase activity; and ubiquitin-like protein conjugating enzyme binding activity. Predicted to be involved in protein polyubiquitination and proteolysis involved in protein catabolic process. Predicted to act upstream of or within several processes, including negative regulation of autophagy; protein destabilization; and regulation of autophagosome assembly. Predicted to be located in endoplasmic reticulum and membrane. Orthologous to human RNF5 (ring finger protein 5). [provided by Alliance of Genome Resources, Dec 2024]

Expression

Biased expression in Kidney (RPKM 216.4), Adrenal (RPKM 112.8) and 9 other tissues See more

Orthologs

human mouse all

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Genomic context

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See Rnf5 in Genome Data Viewer

Location:

20p12

Exon count:

5

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Annotation release | Status | Assembly | Chr | Location
RS_2024_02 | current | GRCr8 (GCF_036323735.1) | 20 | NC_086038.1 (4150032..4152593)
RS_2023_06 | previous assembly | mRatBN7.2 (GCF_015227675.2) | 20 | NC_051355.1 (4145539..4147985)
106 | previous assembly | Rnor_6.0 (GCF_000001895.5) | 20 | NC_005119.4 (4366244..4368690, complement)

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Chromosome 20 - NC_086038.1

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:
NC_086038.1 Chromosome 20 Reference GRCr8

NC_051355.1 Chromosome 20 Reference mRatBN7.2 Primary Assembly

NC_005119.4 Chromosome 20 Reference Rnor_6.0 Primary Assembly

Go to nucleotide: Graphics FASTA GenBank

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Expression

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See details

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

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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Related articles in PubMed

1. The ubiquitin ligase RNF5 regulates antiviral responses by mediating degradation of the adaptor protein MITA. Zhong B, et al. Immunity, 2009 Mar 20. PMID 19285439

2. Regulation of endoplasmic reticulum-associated degradation by RNF5-dependent ubiquitination of JNK-associated membrane protein (JAMP). Tcherpakov M, et al. J Biol Chem, 2009 May 1. PMID 19269966, Free PMC Article

3. RNF185 is a novel E3 ligase of endoplasmic reticulum-associated degradation (ERAD) that targets cystic fibrosis transmembrane conductance regulator (CFTR). El Khouri E, et al. J Biol Chem, 2013 Oct 25. PMID 24019521, Free PMC Article

4. Regulation of ATG4B stability by RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection. Kuang E, et al. PLoS Genet, 2012. PMID 23093945, Free PMC Article

5. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, et al. Genome Res, 2004 Apr. PMID 15060004, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
Submit: New GeneRIF Correction

General gene information

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Markers

AI453961 (e-PCR)

UniSTS:226220

AU026365 (e-PCR)

UniSTS:114352

RH133750 (e-PCR)

UniSTS:217033

RH137557 (e-PCR)

UniSTS:217033

BE119939 (e-PCR)

UniSTS:249306

Homology

NCBI Orthologs
Orthologs from OrthoDB

Clone Names

MGC109637

Gene Ontology Provided by RGD

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Function | Evidence Code | Pubs

enables identical protein binding

ISO
Inferred from Sequence Orthology
more info

enables metal ion binding

IEA
Inferred from Electronic Annotation
more info

enables protein-containing complex binding

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

IEA
Inferred from Electronic Annotation
more info

enables ubiquitin-like protein conjugating enzyme binding

IBA
Inferred from Biological aspect of Ancestor
more info

enables ubiquitin-like protein conjugating enzyme binding

IEA
Inferred from Electronic Annotation
more info

enables ubiquitin-protein transferase activity

ISO
Inferred from Sequence Orthology
more info

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Process | Evidence Code | Pubs

involved_in ERAD pathway

IBA
Inferred from Biological aspect of Ancestor
more info

involved_in ERAD pathway

ISO
Inferred from Sequence Orthology
more info

acts_upstream_of_or_within negative regulation of autophagy

ISO
Inferred from Sequence Orthology
more info

involved_in protein K48-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 catabolic process

ISO
Inferred from Sequence Orthology
more info

acts_upstream_of_or_within protein destabilization

ISO
Inferred from Sequence Orthology
more info

involved_in protein ubiquitination

IEA
Inferred from Electronic Annotation
more info

acts_upstream_of_or_within protein ubiquitination

ISO
Inferred from Sequence Orthology
more info

acts_upstream_of_or_within regulation of autophagosome assembly

ISO
Inferred from Sequence Orthology
more info

acts_upstream_of_or_within response to bacterium

ISO
Inferred from Sequence Orthology
more info

involved_in ubiquitin-dependent protein catabolic process

IBA
Inferred from Biological aspect of Ancestor
more info

involved_in ubiquitin-dependent protein catabolic process

IEA
Inferred from Electronic Annotation
more info

involved_in ubiquitin-dependent protein catabolic process

ISO
Inferred from Sequence Orthology
more info

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Component | Evidence Code | Pubs

located_in endoplasmic reticulum

ISO
Inferred from Sequence Orthology
more info

located_in endoplasmic reticulum membrane

IEA
Inferred from Electronic Annotation
more info

located_in membrane

ISO
Inferred from Sequence Orthology
more info

located_in mitochondrial membrane

IEA
Inferred from Electronic Annotation
more info

located_in plasma membrane

IEA
Inferred from Electronic Annotation
more info

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General protein information

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Preferred Names

E3 ubiquitin-protein ligase RNF5

Names

RING-type E3 ubiquitin transferase RNF5

ing finger protein 5 pseudogene

ring finger protein 5, E3 ubiquitin protein ligase

NP_001102495.1

EC 2.3.2.27

XP_063135456.1

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)

1. NM_001109025.2 → NP_001102495.1 E3 ubiquitin-protein ligase RNF5

See identical proteins and their annotated locations for NP_001102495.1

Status: VALIDATED

Source sequence(s)

BC088341, DY573537

UniProtKB/Swiss-Prot

Q5M807

UniProtKB/TrEMBL

A6KTG9

Related

ENSRNOP00000070056.3, ENSRNOT00000088244.3

Conserved Domains (2) summary

PLN03208
Location:25 → 117

PLN03208; E3 ubiquitin-protein ligase RMA2; Provisional

cd16743
Location:25 → 70

RING-HC_RNF5; RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

This section includes genomic Reference Sequences (RefSeqs) from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. Model RNAs and proteins are also reported here.

Reference GRCr8

Genomic

1. NC_086038.1 Reference GRCr8

Range

4150032..4152593

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

1. XM_063279386.1 → XP_063135456.1 E3 ubiquitin-protein ligase RNF5 isoform X1

UniProtKB/TrEMBL

A0A0G2JWX8, A0A8L2UHC5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

These RefSeqs were suppressed for the cited reason(s). Suppressed RefSeqs do not appear in BLAST databases, related sequence links, or BLAST links (BLink), but may still be retrieved by clicking on their accession.version below.

1. NG_004074.2: Suppressed sequence

Description

NG_004074.2: This RefSeq was permanently suppressed because there is evidence from cDNAs that the locus is transcribed and encodes a protein similar to that identified in other species. NG_004074.2 erroneously represented the str

2. NG_004074.2: Suppressed sequence

Description

NG_004074.2: This RefSeq was permanently suppressed because there is evidence from cDNAs that the locus is transcribed and encodes a protein similar to that identified in other species. NG_004074.2 erroneously represented the str

Related sequences

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Nucleotide | Protein | Strain
Heading | Accession and Version
genomic | BX883044.1 (213864..216159) | None | BN/SsNHsd
genomic | CH474121.1 | EDL83395.1
| EDL83396.1
| EDL83397.1
| EDL83398.1
| EDL83399.1
| EDL83400.1
genomic | JAXUCZ010000020.1 (4150032..4152593) | None | BN/NHsdMcwi
mRNA | BC088341.1 | AAH88341.1
mRNA | DY573537.1 | None

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Protein Accession | Links
GenPept Link | UniProtKB Link
Q5M807.1 | GenPept | UniProtKB/Swiss-Prot:Q5M807

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Additional links

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Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information

Interologous Interaction Database

Interologous Interaction Database

MilliporeSigma

RNF5 products

Molecular Biology Databases

BioGPS

BioGPS

GlyGen glycoinformatics resource

GlyGen glycoinformatics resource

Ingenuity Pathways Analysis

Ingenuity Pathways Analysis

Kyoto Encyclopedia of Genes and Genomes

Kyoto Encyclopedia of Genes and Genomes

OrthoDB catalog of orthologs

Orthologs

PhosphoSitePlus

PhosphoSitePlus® - comprehensive post-translational modification resource

Research Materials

ExactAntigen/Labome

reagents

GenScript latest version of gene cDNA ORF Clone

GenScript latest version of gene cDNA ORF Clone

GeneCopoeia Inc.

Order TALEN/CRISPR clones

OriGene

Order Rnf5 cDNA clone/Protein/Antibody/RNAi

Tools

GeneMANIA

GeneMANIA

Miscellaneous

Reactome

Reactome Entity:Q5M807

Reactome Event:Transport of small molecules

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Supplemental Content

Table of contents

Summary

Genomic context

Genomic regions, transcripts, and products

Expression

Bibliography

General gene information
Markers, Clone Names, Homology, Gene Ontology

General protein information

NCBI Reference Sequences (RefSeq)

Related sequences

Additional links

Genome Browsers

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Related information

BioProjects
BioProjects related to a gene

BioSystems
BioSystems

Conserved Domains
Related CDD

Full text in PMC
PMC links

Full text in PMC_nucleotide
Full text in PubMedCentral identified from shared sequence links

Functional Class
Functional class of the sequence domain architecture

Gene neighbors
Overlapping genes and two nearest non-overlapping genes on either side

Genome
Related Genome

GEO Profiles
Related GEO

Nucleotide
Link to related Nucleotide entry

Probe
Related Probe entry

Protein
Link to related protein entry

PubChem Compound
PubChem Compounds

PubChem Substance
PubChem Substances

PubMed
Link to related PubMed entry

PubMed(nucleotide/PMC)
Citations in PubMed identified from shared sequence and PMC links.

RefSeq Proteins
Link to Protein RefSeqs

RefSeq RNAs
Link to Nucleotide RefSeq RNAs

Taxonomy
Link to related taxonomy entry

Links to other resources

RGD

EnsemblRapid

AllianceGenome

UCSC

MGC

KEGG

Reactome

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Rnf5 ring finger protein 5 [Rattus norvegicus]
Rnf5 ring finger protein 5 [Rattus norvegicus]
Gene ID:407784

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