Ubr4 ubiquitin protein ligase E3 component n-recognin 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ubr4provided by RGD
Official Full Name: ubiquitin protein ligase E3 component n-recognin 4provided by RGD
Primary source: RGD:1563121
See related: EnsemblRapid:ENSRNOG00000018183 AllianceGenome:RGD:1563121
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: Rbaf600
Summary: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of HRI-mediated signaling; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein polyubiquitination. Predicted to act upstream of or within protein catabolic process and protein stabilization. Predicted to be located in endosome. Predicted to be active in centrosome; cytosol; and nucleoplasm. Orthologous to human UBR4 (ubiquitin protein ligase E3 component n-recognin 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 264.4), Adrenal (RPKM 251.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 110

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (156919029..157027127)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (151635825..151743931)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (157848162..157956137)

Chromosome 5 - NC_086023.1 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?

Data indicate a distinct mechanism of prevention of Ca(2+)/calmodulin-dependent kinase IIalpha (CaMKIIalpha) aggregation by E3 ubiquitin-protein ligase p600 (UBR4).
Title: p600 stabilizes microtubules to prevent the aggregation of CaMKIIα during photoconductive stimulation.
p600 counteracts specific Ca(2+)-induced death pathways through regulation of Ca(2+) homeostasis and signaling.
Title: A Ca2+-dependent mechanism of neuronal survival mediated by the microtubule-associated protein p600.

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

RH138653 (e-PCR)
- UniSTS:220740

Ubr4 (e-PCR), detects polymorphism
- UniSTS:547169

AI136251 (e-PCR)
- UniSTS:243840

RH136771 (e-PCR)
- UniSTS:218860

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calmodulin binding	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 ligase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin-protein transferase 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 cytoplasm protein quality control	ISO Inferred from Sequence Orthology more info
involved_in cytoplasm protein quality control	ISS Inferred from Sequence or Structural Similarity more info
involved_in cytoplasm protein quality control by the ubiquitin-proteasome system	IEA Inferred from Electronic Annotation more info
involved_in cytoplasm protein quality control by the ubiquitin-proteasome system	ISO Inferred from Sequence Orthology more info
involved_in cytoplasm protein quality control by the ubiquitin-proteasome system	ISS Inferred from Sequence or Structural Similarity more info
involved_in endosome organization	IEA Inferred from Electronic Annotation more info
involved_in endosome organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of HRI-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of HRI-mediated signaling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of HRI-mediated signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of fatty acid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of fatty acid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of autophagy	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation more info
involved_in protein K11-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K11-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K27-linked ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K27-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K27-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K48-linked ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K48-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K48-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein branched polyubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein branched polyubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein branched polyubiquitination	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein stabilization	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in response to oxidative stress	IEA Inferred from Electronic Annotation more info
involved_in response to oxidative stress	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	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway	ISO Inferred from Sequence Orthology more info

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

General protein information

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Preferred Names: E3 ubiquitin-protein ligase UBR4

Names: N-recognin-4; RING-type E3 ubiquitin transferase UBR4; ZUBR1; retinoblastoma-associated factor 600; zinc finger UBR1-type protein 1

NP_001382037.1

EC 2.3.2.27

XP_063143863.1

EC 2.3.2.27

XP_063143864.1

EC 2.3.2.27

XP_063143865.1

EC 2.3.2.27

XP_063143866.1

EC 2.3.2.27

XP_063143867.1

EC 2.3.2.27

XP_063143868.1

EC 2.3.2.27

XP_063143869.1

EC 2.3.2.27

XP_063143870.1

EC 2.3.2.27

XP_063143871.1

EC 2.3.2.27

XP_063143872.1

EC 2.3.2.27

XP_063143873.1

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_001395108.1 → NP_001382037.1 E3 ubiquitin-protein ligase UBR4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A0G2JU89

Related

ENSRNOP00000069008.3, ENSRNOT00000082138.3

Conserved Domains (3) summary

smart00396
Location:1661 → 1728

ZnF_UBR1; Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway

pfam12773
Location:3659 → 3703

DZR; Double zinc ribbon

pfam13764
Location:4366 → 5162

E3_UbLigase_R4; E3 ubiquitin-protein ligase UBR4

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_086023.1 Reference GRCr8

Range

156919029..157027127

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287801.1 → XP_063143871.1 E3 ubiquitin-protein ligase UBR4 isoform X9
XM_063287793.1 → XP_063143863.1 E3 ubiquitin-protein ligase UBR4 isoform X1
XM_063287796.1 → XP_063143866.1 E3 ubiquitin-protein ligase UBR4 isoform X4
XM_063287794.1 → XP_063143864.1 E3 ubiquitin-protein ligase UBR4 isoform X2
XM_063287798.1 → XP_063143868.1 E3 ubiquitin-protein ligase UBR4 isoform X6
XM_063287799.1 → XP_063143869.1 E3 ubiquitin-protein ligase UBR4 isoform X7
XM_063287797.1 → XP_063143867.1 E3 ubiquitin-protein ligase UBR4 isoform X5
XM_063287795.1 → XP_063143865.1 E3 ubiquitin-protein ligase UBR4 isoform X3

Related

ENSRNOP00000032156.5, ENSRNOT00000039663.7
XM_063287800.1 → XP_063143870.1 E3 ubiquitin-protein ligase UBR4 isoform X8
XM_063287803.1 → XP_063143873.1 E3 ubiquitin-protein ligase UBR4 isoform X11
XM_063287802.1 → XP_063143872.1 E3 ubiquitin-protein ligase UBR4 isoform X10

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001039026.1: Suppressed sequence

Description

NM_001039026.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.