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UBE2E3 ubiquitin conjugating enzyme E2 E3 [ Homo sapiens (human) ]

Gene ID: 10477, updated on 7-Apr-2024

Summary

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Official Symbol
UBE2E3provided by HGNC
Official Full Name
ubiquitin conjugating enzyme E2 E3provided by HGNC
Primary source
HGNC:HGNC:12479
See related
Ensembl:ENSG00000170035 MIM:604151; AllianceGenome:HGNC:12479
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UBCH9; UbcM2
Summary
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. The encoded protein shares 100% sequence identity with the mouse and rat counterparts, which indicates that this enzyme is highly conserved in eukaryotes. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jun 2013]
Expression
Ubiquitous expression in gall bladder (RPKM 6.0), thyroid (RPKM 5.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
2q31.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (180980360..181063425)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (181470000..181553425)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (181845087..181928152)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene SWI/SNF complex antagonist associated with prostate cancer 1 Neighboring gene ferritin heavy chain 1 pseudogene 20 Neighboring gene ribosomal protein L27a pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16822 Neighboring gene UBE2E3 divergent transcript Neighboring gene uncharacterized LOC107985831 Neighboring gene NANOG hESC enhancer GRCh37_chr2:181971702-181972203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16823 Neighboring gene long intergenic non-protein coding RNA 1934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16824 Neighboring gene microRNA 4437

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Loss of the ubiquitin conjugating enzyme UBE2E3 induces cellular senescence. Plafker KS, et al. Redox Biol, 2018 Jul. PMID 29879550, Free PMC Article
  2. The human ubiquitin conjugating enzyme, UBE2E3, is required for proliferation of retinal pigment epithelial cells. Plafker KS, et al. Invest Ophthalmol Vis Sci, 2008 Dec. PMID 18614808, Free PMC Article
  3. Control of NF-kappa B transcriptional activation by signal induced proteolysis of I kappa B alpha. Hay RT, et al. Philos Trans R Soc Lond B Biol Sci, 1999 Sep 29. PMID 10582246, Free PMC Article
  4. cDNA cloning, characterization, and chromosome mapping of UBE2E3 (alias UbcH9), encoding an N-terminally extended human ubiquitin-conjugating enzyme. Ito K, et al. Cytogenet Cell Genet, 1999. PMID 10343118
  5. Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. Li S, et al. J Biol Chem, 2015 Dec 18. PMID 26475854, Free PMC Article

See all (93) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Cells depleted of UBE2E3 become senescent in the absence of overt DNA damage and have a distinct senescence-associated secretory phenotype, increased mitochondrial and lysosomal mass, an increased sensitivity to mitochondrial and lysosomal poisons, and an increased basal autophagic flux.
    Title: Loss of the ubiquitin conjugating enzyme UBE2E3 induces cellular senescence.
  2. Data indicate that ubiquitin-conjugating enzyme UBE2E3 and importin 11 (Imp-11)promote the nuclear accumulation and activity of transcription factor NF-E2 (Nrf2) by restricting the transcription factor from partitioning to the mitochondria.
    Title: The ubiquitin-conjugating enzyme UBE2E3 and its import receptor importin-11 regulate the localization and activity of the antioxidant transcription factor NRF2.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. UBE2E3 is essential for the proliferation of RPE-1 cells and is downregulated during RPE layer maturation in the developing mouse eye.
    Title: The human ubiquitin conjugating enzyme, UBE2E3, is required for proliferation of retinal pigment epithelial cells.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study on obesity and obesity-related traits.
EBI GWAS Catalog
Multiple common variants for celiac disease influencing immune gene expression.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of ubiquitin-conjugating enzyme E2E 3 (UBE2E3) by siRNA inhibits HIV-1 replication in CD4+/CCR5+/CXCR4+ TZM-bl HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin conjugating enzyme activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein K11-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein K11-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K48-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K63-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein K63-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ubiquitin-conjugating enzyme E2 E3
Names
E2 ubiquitin-conjugating enzyme E3
ubiquitin carrier protein E3
ubiquitin conjugating enzyme E2E 3
ubiquitin-conjugating enzyme E2-23 kDa
ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)
ubiquitin-conjugating enzyme E2E 3 (homologous to yeast UBC4/5)
ubiquitin-protein ligase E3
NP_001265483.1
NP_001265484.1
NP_006348.1
NP_872619.1
XP_005246301.1
XP_016858656.1
XP_054196155.1
XP_054196156.1

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_001278554.2 → NP_001265483.1  ubiquitin-conjugating enzyme E2 E3

    See identical proteins and their annotated locations for NP_001265483.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC104076, AK314145, BU608985, DA568152
    Consensus CDS
    CCDS2282.1
    UniProtKB/Swiss-Prot
    B2RAD6, D3DPG3, Q5U0R7, Q7Z4W4, Q969T4
    UniProtKB/TrEMBL
    A0A1B0GX65
    Related
    ENSP00000473623.1, ENST00000602710.5
    Conserved Domains (1) summary
    pfam00179
    Location:65 → 202
    UQ_con; Ubiquitin-conjugating enzyme

  2. NM_001278555.2 → NP_001265484.1  ubiquitin-conjugating enzyme E2 E3

    See identical proteins and their annotated locations for NP_001265484.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC104076, BC092407, BI257596, BQ932163, BU608985
    Consensus CDS
    CCDS2282.1
    UniProtKB/Swiss-Prot
    B2RAD6, D3DPG3, Q5U0R7, Q7Z4W4, Q969T4
    UniProtKB/TrEMBL
    A0A1B0GX65
    Related
    ENSP00000376215.2, ENST00000392415.6
    Conserved Domains (1) summary
    pfam00179
    Location:65 → 202
    UQ_con; Ubiquitin-conjugating enzyme

  3. NM_006357.4 → NP_006348.1  ubiquitin-conjugating enzyme E2 E3

    See identical proteins and their annotated locations for NP_006348.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    BC092407, BU608985, DB458228
    Consensus CDS
    CCDS2282.1
    UniProtKB/Swiss-Prot
    B2RAD6, D3DPG3, Q5U0R7, Q7Z4W4, Q969T4
    UniProtKB/TrEMBL
    A0A1B0GX65
    Related
    ENSP00000386788.3, ENST00000410062.9
    Conserved Domains (1) summary
    pfam00179
    Location:65 → 202
    UQ_con; Ubiquitin-conjugating enzyme

  4. NM_182678.3 → NP_872619.1  ubiquitin-conjugating enzyme E2 E3

    See identical proteins and their annotated locations for NP_872619.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC104076, BC092407, BQ932163, BU608985
    Consensus CDS
    CCDS2282.1
    UniProtKB/Swiss-Prot
    B2RAD6, D3DPG3, Q5U0R7, Q7Z4W4, Q969T4
    UniProtKB/TrEMBL
    A0A1B0GX65
    Related
    ENSP00000473639.1, ENST00000602959.5
    Conserved Domains (1) summary
    pfam00179
    Location:65 → 202
    UQ_con; Ubiquitin-conjugating enzyme

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    180980360..181063425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003167.3 → XP_016858656.1  ubiquitin-conjugating enzyme E2 E3 isoform X2

  2. XM_005246244.3 → XP_005246301.1  ubiquitin-conjugating enzyme E2 E3 isoform X1

    See identical proteins and their annotated locations for XP_005246301.1

    UniProtKB/Swiss-Prot
    B2RAD6, D3DPG3, Q5U0R7, Q7Z4W4, Q969T4
    UniProtKB/TrEMBL
    A0A1B0GX65
    Conserved Domains (1) summary
    pfam00179
    Location:65 → 202
    UQ_con; Ubiquitin-conjugating enzyme

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    181470000..181553425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340181.1 → XP_054196156.1  ubiquitin-conjugating enzyme E2 E3 isoform X2

  2. XM_054340180.1 → XP_054196155.1  ubiquitin-conjugating enzyme E2 E3 isoform X1

    UniProtKB/Swiss-Prot
    B2RAD6, D3DPG3, Q5U0R7, Q7Z4W4, Q969T4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969T4.1 GenPept UniProtKB/Swiss-Prot:Q969T4

Gene LinkOut

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