Ube2d3 ubiquitin-conjugating enzyme E2D 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ube2d3provided by RGD
Official Full Name: ubiquitin-conjugating enzyme E2D 3provided by RGD
Primary source: RGD:619912
See related: EnsemblRapid:ENSRNOG00000013741 AllianceGenome:RGD:619912
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables ubiquitin-protein transferase activity. Involved in cellular response to cadmium ion; cellular response to mercury ion; and ubiquitin-dependent protein catabolic process. Predicted to be located in endosome membrane and plasma membrane. Predicted to be active in nucleus. Orthologous to human UBE2D3 (ubiquitin conjugating enzyme E2 D3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 1032.7), Heart (RPKM 896.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q43

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (226543194..226571001)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (223868397..223899606)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (240626198..240655874)

Chromosome 2 - NC_086020.1 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?

UBE2D3 contributes to myocardial ischemia-reperfusion injury by regulating autophagy in dependence of p62/SQSTM1.
Title: UBE2D3 contributes to myocardial ischemia-reperfusion injury by regulating autophagy in dependence of p62/SQSTM1.
ubiquitin-conjugating enzyme E2D 3 (UBE2D3), cAMP-dependent protein kinase C beta subunit (PKCbeta), excitatory amino acid carrier 1 (EAAC1), and ferritin heavy polypeptide 1 (Fth1), that were upregulated after a 48-h fast
Title: Identification of fasting-induced genes in the rat hypothalamus: relationship with neuroprotection.

Submit: New GeneRIF Correction

General gene information

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Markers

AU027051 (e-PCR)
- UniSTS:113679

RH128490 (e-PCR)
- UniSTS:211798

BE116708 (e-PCR)
- UniSTS:248531

RH125441 (e-PCR)
- UniSTS:162261

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin conjugating enzyme activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin conjugating enzyme activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin conjugating enzyme activity	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cellular response to cadmium ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to mercury ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of protein targeting to mitochondrion	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology 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	IBA Inferred from Biological aspect of Ancestor 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 K48-linked ubiquitination	IBA Inferred from Biological aspect of Ancestor 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 K6-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K6-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein monoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	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	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin-conjugating enzyme E2 D3

Names: (E3-independent) E2 ubiquitin-conjugating enzyme D3; E2 ubiquitin-conjugating enzyme D3; E2(17)KB 3; PAPase; phosphoarginine phosphatase; ubiquitin carrier protein D3; ubiquitin-conjugating enzyme E2(17)KB 3; ubiquitin-conjugating enzyme E2-17 kDa 3; ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast); ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5); ubiquitin-protein ligase D3

NP_112516.1

EC 2.3.2.23

EC 2.3.2.24

XP_006233397.1

EC 2.3.2.23

EC 2.3.2.24

XP_063138705.1

EC 2.3.2.23

EC 2.3.2.24

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_031237.1 → NP_112516.1 ubiquitin-conjugating enzyme E2 D3

See identical proteins and their annotated locations for NP_112516.1

Status: PROVISIONAL

Source sequence(s)

AB006852

UniProtKB/Swiss-Prot

P61078

UniProtKB/TrEMBL

A0A0G2K739, A6HVX6

Related

ENSRNOP00000060962.3, ENSRNOT00000066204.5

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...

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_086020.1 Reference GRCr8

Range

226543194..226571001

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006233335.4 → XP_006233397.1 ubiquitin-conjugating enzyme E2 D3 isoform X1

See identical proteins and their annotated locations for XP_006233397.1

UniProtKB/TrEMBL

A0A0G2K739, A0A8I5ZTF1, A6HVY0

Related

ENSRNOP00000080614.1, ENSRNOT00000103636.2

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
XM_063282635.1 → XP_063138705.1 ubiquitin-conjugating enzyme E2 D3 isoform X2

UniProtKB/TrEMBL

A0A0G2JV72