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UBE2L3 ubiquitin conjugating enzyme E2 L3 [ Homo sapiens (human) ]

Gene ID: 7332, updated on 3-Nov-2024

Summary

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Official Symbol
UBE2L3provided by HGNC
Official Full Name
ubiquitin conjugating enzyme E2 L3provided by HGNC
Primary source
HGNC:HGNC:12488
See related
Ensembl:ENSG00000185651 MIM:603721; AllianceGenome:HGNC:12488
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
E2-F1; L-UBC; UBCH7; UbcM4
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 (E1s), ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s). This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is demonstrated to participate in the ubiquitination of p53, c-Fos, and the NF-kB precursor p105 in vitro. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]
Expression
Ubiquitous expression in brain (RPKM 19.5), urinary bladder (RPKM 19.0) and 25 other tissues See more
Orthologs
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Genomic context

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See UBE2L3 in Genome Data Viewer
Location:
22q11.21
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (21549447..21624034)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (21962924..22037518)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (21903736..21978323)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene small Cajal body-specific RNA 18 Neighboring gene RN7SK pseudogene 221 Neighboring gene RIMS binding protein 3C Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21908512-21908665 Neighboring gene Sharpr-MPRA regulatory region 10827 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21914232-21914792 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21920997-21921184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21945023-21945836 Neighboring gene VISTA enhancer hs2026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21977501-21978034 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21979673-21979941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21982145-21982752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21986781-21987280 Neighboring gene YdjC chitooligosaccharide deacetylase homolog Neighboring gene coiled-coil domain containing 116

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 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. UBE2L3 expression in human gastric cancer and its clinical significance. Zhang X, et al. J Cancer Res Clin Oncol, 2024 Apr 24. PMID 38656363, Free PMC Article
  2. Purification and characterization of a novel species of ubiquitin-carrier protein, E2, that is involved in degradation of non-"N-end rule" protein substrates. Blumenfeld N, et al. J Biol Chem, 1994 Apr 1. PMID 8144544
  3. Fine-mapping, genomic organization, and transcript analysis of the human ubiquitin-conjugating enzyme gene UBE2L3. Moynihan TP, et al. Genomics, 1998 Jul 1. PMID 9693040
  4. The autoimmune disease risk allele of UBE2L3 in African American patients with systemic lupus erythematosus: a recessive effect upon subphenotypes. Agik S, et al. J Rheumatol, 2012 Jan. PMID 22045845, Free PMC Article
  5. Association of UBE2L3 polymorphisms with diffuse cutaneous systemic sclerosis in a Japanese population. Hasebe N, et al. Ann Rheum Dis, 2012 Jul. PMID 22294623

See all (394) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of Ubiquitin-conjugating enzyme E2 (UBE2) in two immune-mediated inflammatory skin diseases: a mendelian randomization analysis.
    Title: Role of Ubiquitin-conjugating enzyme E2 (UBE2) in two immune-mediated inflammatory skin diseases: a mendelian randomization analysis.
  2. UBE2L3 expression in human gastric cancer and its clinical significance.
    Title: UBE2L3 expression in human gastric cancer and its clinical significance.
  3. The E3 ligase SMURF1 stabilizes p27 via UbcH7 catalyzed K29-linked ubiquitin chains to promote cell migration SMURF1-UbcH7 K29 ubiquitination of p27 and cell migration.
    Title: The E3 ligase SMURF1 stabilizes p27 via UbcH7 catalyzed K29-linked ubiquitin chains to promote cell migration SMURF1-UbcH7 K29 ubiquitination of p27 and cell migration.
  4. The membrane-associated ubiquitin ligase MARCHF8 stabilizes the human papillomavirus oncoprotein E7 by degrading CUL1 and UBE2L3 in head and neck cancer.
    Title: The membrane-associated ubiquitin ligase MARCHF8 stabilizes the human papillomavirus oncoprotein E7 by degrading CUL1 and UBE2L3 in head and neck cancer.
  5. UBE2L3 Reduces TRIM21 Expression and IL-1beta Secretion in Epidermal Keratinocytes and Improves Psoriasis-Like Skin.
    Title: UBE2L3 Reduces TRIM21 Expression and IL-1β Secretion in Epidermal Keratinocytes and Improves Psoriasis-Like Skin.
  6. UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus.
    Title: UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus.
  7. UBE2L3 promotes squamous cell carcinoma progression in the oral cavity and hypopharynx via activating the NF-kappaB signaling by increasing IkappaBalpha degradation.
    Title: UBE2L3 promotes squamous cell carcinoma progression in the oral cavity and hypopharynx via activating the NF-κB signaling by increasing IκBα degradation.
  8. Variants on the UBE2L3/YDJC Autoimmune Disease Risk Haplotype Increase UBE2L3 Expression by Modulating CCCTC-Binding Factor and YY1 Binding.
    Title: Variants on the UBE2L3/YDJC Autoimmune Disease Risk Haplotype Increase UBE2L3 Expression by Modulating CCCTC-Binding Factor and YY1 Binding.
  9. Synergistic activation of NF-kappaB by TNFAIP3 (A20) reduction and UBE2L3 (UBCH7) augment that synergistically elevate lupus risk.
    Title: Synergistic activation of NF-κB by TNFAIP3 (A20) reduction and UBE2L3 (UBCH7) augment that synergistically elevate lupus risk.
  10. Overexpression of ubiquitin-conjugating enzyme E2 L3 in hepatocellular carcinoma potentiates apoptosis evasion by inhibiting the GSK3beta/p65 pathway.
    Title: Overexpression of ubiquitin-conjugating enzyme E2 L3 in hepatocellular carcinoma potentiates apoptosis evasion by inhibiting the GSK3β/p65 pathway.
Submit: New GeneRIF Correction See all GeneRIFs (40)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
EBI GWAS Catalog
Genome-wide association study of hematological and biochemical traits in a Japanese population.
EBI GWAS Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
EBI GWAS Catalog
Multiple common variants for celiac disease influencing immune gene expression.
EBI GWAS Catalog
New loci associated with chronic hepatitis B virus infection in Han Chinese.
EBI GWAS Catalog
Seventy-five genetic loci influencing the human red blood cell.
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 E2L 3 (UBE2L3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef In the presence of Nef, lipid raft Cdc42 is activated and forms a ternary complex between the c-Cbl-interacting protein p85Cool-1/betaPix and c-Cbl, displacing UbcH7 from rafts PubMed
nef HIV-1 Nef excludes E2 ubiquitin-conjugating enzyme UbcH7, which acts in conjunction with c-Cbl, from lipid rafts in CD4 T cells; this Nef-mediated exclusion is associated with failure of ubiquitination of activated Vav 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 RNA binding HDA PubMed 
enables enzyme binding TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin conjugating enzyme activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin conjugating enzyme activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin-protein transferase activator activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables ubiquitin-protein transferase activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to glucocorticoid stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to steroid hormone stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of protein targeting to mitochondrion HMP PubMed 
involved_in positive regulation of protein ubiquitination IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of ubiquitin-protein transferase activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
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 modification process TAS
Traceable Author Statement
more info
 PubMed 
involved_in protein polyubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
part_of ubiquitin ligase complex TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
ubiquitin-conjugating enzyme E2 L3
Names
E2 ubiquitin-conjugating enzyme L3
ubiquitin carrier protein L3
ubiquitin conjugating enzyme E2L 3
ubiquitin-conjugating enzyme E2-F1
ubiquitin-conjugating enzyme UBCH7
ubiquitin-protein ligase L3
NP_001243284.1
NP_001243285.1
NP_003338.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001256355.1 → NP_001243284.1  ubiquitin-conjugating enzyme E2 L3 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (4).
    Source sequence(s)
    AJ000519, AK299985
    Consensus CDS
    CCDS58795.1
    UniProtKB/Swiss-Prot
    P68036
    Related
    ENSP00000400906.2, ENST00000458578.6
    Conserved Domains (2) summary
    smart00212
    Location:67 → 207
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic domain homologues
    COG5078
    Location:67 → 208
    COG5078; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]

  2. NM_001256356.2 → NP_001243285.1  ubiquitin-conjugating enzyme E2 L3 isoform 3

    See identical proteins and their annotated locations for NP_001243285.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' splice site, lacks an alternate exon, and initiates translation from a downstream start site, compared to variant 4. It encodes a shorter and distinct N-terminus in isoform 3, compared to isoform 4.
    Source sequence(s)
    AJ000519, AK293179, BU584304
    Consensus CDS
    CCDS58796.1
    UniProtKB/Swiss-Prot
    P68036
    Related
    ENSP00000445931.1, ENST00000545681.2
    Conserved Domains (1) summary
    pfam00179
    Location:9 → 112
    UQ_con; Ubiquitin-conjugating enzyme

  3. NM_003347.4 → NP_003338.1  ubiquitin-conjugating enzyme E2 L3 isoform 1

    See identical proteins and their annotated locations for NP_003338.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses an alternate 5' splice site and downstream translational start site, compared to variant 4. It encodes a shorter and distinct N-terminus in isoform 1, compared to isoform 4.
    Source sequence(s)
    AJ000519, BU584304
    Consensus CDS
    CCDS13790.1
    UniProtKB/Swiss-Prot
    B2R4A7, B4DDG1, B4DSZ4, E7EWS7, P51966, P68036, P70653, Q9HAV1
    UniProtKB/TrEMBL
    A8K4W8
    Related
    ENSP00000344259.5, ENST00000342192.9
    Conserved Domains (1) summary
    smart00212
    Location:6 → 149
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic domain homologues

RNA

  1. NR_028436.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon, compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AJ000519, BU567707, BU584304

  2. NR_046082.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate exon, compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AJ000519, AK125396, AP000558
    Related
    ENST00000496722.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    21549447..21624034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    21962924..22037518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_198157.1: Suppressed sequence

    Description
    NM_198157.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P68036.1 GenPept UniProtKB/Swiss-Prot:P68036

Gene LinkOut

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