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

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Ube4b ubiquitination factor E4B [ Rattus norvegicus (Norway rat) ]
Gene ID: 298652, updated on 9-Dec-2024

Download Datasets

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.

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Summary

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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

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See Ube4b in Genome Data Viewer

Location:

5q36

Exon count:

29

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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)

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Chromosome 5 - NC_086023.1

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:
NC_086023.1 Chromosome 5 Reference GRCr8

NC_051340.1 Chromosome 5 Reference mRatBN7.2 Primary Assembly

NC_005104.4 Chromosome 5 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 WldS gene delays axonal but not somatic degeneration in a rat glaucoma model. Beirowski B, et al. Eur J Neurosci, 2008 Sep. PMID 18783366

2. The ubiquitin ligase UBE4B regulates amyloid precursor protein ubiquitination, endosomal trafficking, and amyloid β42 generation and secretion. Gireud-Goss M, et al. Mol Cell Neurosci, 2020 Oct. PMID 32841720, Free PMC Article

3. Characterization of the mouse gene for the U-box-type ubiquitin ligase UFD2a. Kaneko C, et al. Biochem Biophys Res Commun, 2003 Jan 10. PMID 12504083

4. Structural and functional characterization of the monomeric U-box domain from E4B. Nordquist KA, et al. Biochemistry, 2010 Jan 19. PMID 20017557, Free PMC Article

5. Functional regulation of FEZ1 by the U-box-type ubiquitin ligase E4B contributes to neuritogenesis. Okumura F, et al. J Biol Chem, 2004 Dec 17. PMID 15466860

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

1. 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.

2. 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.

3. 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.

Submit: New GeneRIF Correction

Interactions

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Products | Interactant | Other Gene | Complex | Source | Pubs | Description
BioGRID:255973 | BioGRID:202374 | Mapk11 | | BioGRID | PubMed | Proximity Label-MS

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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

Homology

NCBI Orthologs
Orthologs from OrthoDB

Gene Ontology Provided by RGD

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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

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Items 1 - 14 of 14

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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

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Items 1 - 5 of 5

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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

Items 1 - 5 of 5

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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)

1. 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

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_086023.1 Reference GRCr8

Range

165049897..165153572 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

1. 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

2. XM_017593310.3 → XP_017448799.1 ubiquitin conjugation factor E4 B isoform X2

UniProtKB/TrEMBL

A0A8I6GKR7

Related

ENSRNOP00000093656.2, ENSRNOT00000118861.2

Related sequences

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Nucleotide | Protein | Strain
Heading | Accession and Version
genomic | JAXUCZ010000005.1 (165049897..165153572) | None | BN/NHsdMcwi

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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

MilliporeSigma

UBE4B products

Molecular Biology Databases

Bgee database

Ube4b gene expression

BioGPS

BioGPS

CTD: Comparative Toxicogenomics Database

CTD: Comparative Toxicogenomics Database - UBE4B

GlyGen glycoinformatics resource

GlyGen glycoinformatics resource

Ingenuity Pathways Analysis

Ingenuity Pathways Analysis

Kyoto Encyclopedia of Genes and Genomes

Kyoto Encyclopedia of Genes and Genomes

OMA Browser: Orthologous MAtrix

OMA Browser: Orthologous MAtrix

OMA Browser: Orthologous MAtrix

OMA Browser: Orthologous MAtrix

OrthoDB catalog of orthologs

Orthologs

PhosphoSitePlus

PhosphoSitePlus® - comprehensive post-translational modification resource

Research Materials

Addgene Non-profit plasmid repository

Get Plasmids - Addgene

ExactAntigen/Labome

reagent review

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 UBE4B cDNA clone/Protein/Antibody/RNAi

Tools

GeneMANIA

GeneMANIA

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Supplemental Content

Table of contents

Summary

Genomic context

Genomic regions, transcripts, and products

Expression

Bibliography

Interactions

General gene information
Markers, 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

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 (GeneRIF)
Link to related PubMed article from GeneRIFs

RefSeq Proteins
Link to Protein RefSeqs

RefSeq RNAs
Link to Nucleotide RefSeq RNAs

Taxonomy
Link to related taxonomy entry

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Ube4b ubiquitination factor E4B [Rattus norvegicus]
Ube4b ubiquitination factor E4B [Rattus norvegicus]
Gene ID:298652

Gene

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