Ube4b ubiquitination factor E4B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ube4bprovided by RGD
Official Full Name: ubiquitination factor E4Bprovided by RGD
Primary source: RGD:1304738
See related: EnsemblRapid:ENSRNOG00000014986 AllianceGenome:RGD:1304738
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: ufd2a
Summary: Enables ATPase binding activity. Predicted to be involved in several processes, including ERAD pathway; granzyme-mediated apoptotic signaling pathway; and protein polyubiquitination. Predicted to act upstream of or within several processes, including proteasome-mediated ubiquitin-dependent protein catabolic process; protein ubiquitination; and ventricular trabecula myocardium morphogenesis. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human UBE4B (ubiquitination factor E4B). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 135.0), Adrenal (RPKM 124.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (165049897..165153572, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (159766829..159870509, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (166156033..166259069, complement)

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
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?

The ubiquitin ligase UBE4B regulates amyloid precursor protein ubiquitination, endosomal trafficking, and amyloid beta42 generation and secretion.
Title: The ubiquitin ligase UBE4B regulates amyloid precursor protein ubiquitination, endosomal trafficking, and amyloid β42 generation and secretion.
Data show that Wld(S) delays optic nerve (ON)axonal degeneration in experimental rat glaucoma for at least 2 weeks, especially in proximal ON where wild-type axons are most severely affected.
Title: The WldS gene delays axonal but not somatic degeneration in a rat glaucoma model.
E4B serves as a ubiquitin ligase for FEZ1 and thereby regulates its function but not its degradation
Title: Functional regulation of FEZ1 by the U-box-type ubiquitin ligase E4B contributes to neuritogenesis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU014668 (e-PCR)
- UniSTS:159321

R75060 (e-PCR)
- UniSTS:125532

D5Rat48 (e-PCR)
- UniSTS:118917

BF399470 (e-PCR)
- UniSTS:247695

AW916095 (e-PCR)
- UniSTS:261867

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-ubiquitin ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-ubiquitin ligase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in ERAD pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in granzyme-mediated apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein autoubiquitination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein monoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein polyubiquitination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in response to UV	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to endoplasmic reticulum stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular trabecula myocardium morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of ubiquitin ligase complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin conjugation factor E4 B

Names: ubiquitination factor E4B (UFD2 homolog, yeast); ubiquitination factor E4B, UFD2 homolog

NP_001258127.1

EC 2.3.2.27

XP_006239449.1

EC 2.3.2.27

XP_017448799.1

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_001271198.2 → NP_001258127.1 ubiquitin conjugation factor E4 B

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6G4J1, F1M8V2

Related

ENSRNOP00000052435.4, ENSRNOT00000055572.7

Conserved Domains (2) summary

pfam04564
Location:1099 → 1169

U-box; U-box domain

pfam10408
Location:462 → 1082

Ufd2P_core; Ubiquitin elongating factor core

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

165049897..165153572 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006239387.5 → XP_006239449.1 ubiquitin conjugation factor E4 B isoform X1

UniProtKB/TrEMBL

A0A8I6GAW9

Related

ENSRNOP00000084700.2, ENSRNOT00000116191.2

Conserved Domains (2) summary

pfam04564
Location:1314 → 1384

U-box; U-box domain

pfam10408
Location:677 → 1297

Ufd2P_core; Ubiquitin elongating factor core
XM_017593310.3 → XP_017448799.1 ubiquitin conjugation factor E4 B isoform X2

UniProtKB/TrEMBL

A0A8I6GKR7

Related

ENSRNOP00000093656.2, ENSRNOT00000118861.2