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

Gene ID: 298652, updated on 10-Jul-2024

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 cellular protein metabolic process; granzyme-mediated apoptotic signaling pathway; and response to UV. 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, Apr 2022]
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
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_086023.1Genomic Context describing neighboring genes Neighboring gene kinesin family member 1B Neighboring gene uncharacterized LOC134487037 Neighboring gene uncharacterized LOC102547502 Neighboring gene retinol binding protein 7 Neighboring gene uncharacterized LOC134479087 Neighboring gene nicotinamide nucleotide adenylyltransferase 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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. 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
  4. 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
  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

General gene information

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Markers

Homology

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
XP_006239449.1
XP_017448799.1

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

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
Nucleotide Protein Strain
Heading Accession and Version

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