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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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