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

Gene ID: 7332, updated on 11-Sep-2019

Summary

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
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

Genomic context

See UBE2L3 in Genome Data Viewer
Location:
22q11.21
Exon count:
6
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (21549447..21624034)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (21903736..21978323)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol 4-kinase alpha pseudogene 2 Neighboring gene RN7SK pseudogene 221 Neighboring gene RIMS binding protein 3C Neighboring gene VISTA enhancer hs2026 Neighboring gene coiled-coil domain containing 116 Neighboring gene YdjC chitooligosaccharide deacetylase homolog

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
NHGRI GWA Catalog
Genome-wide association study of hematological and biochemical traits in a Japanese population.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA 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.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog
New loci associated with chronic hepatitis B virus infection in Han Chinese.
NHGRI GWA Catalog
Seventy-five genetic loci influencing the human red blood cell.
NHGRI GWA Catalog

HIV-1 interactions

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 BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Alpha-synuclein signaling, organism-specific biosystem (from Pathway Interaction Database)
    Alpha-synuclein signaling, organism-specific biosystem
    Alpha-synuclein signaling
  • Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystem (from REACTOME)
    Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystemIntracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T ...
  • BARD1 signaling events, organism-specific biosystem (from Pathway Interaction Database)
    BARD1 signaling events, organism-specific biosystem
    BARD1 signaling events
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • E3 ubiquitin ligases ubiquitinate target proteins, organism-specific biosystem (from REACTOME)
    E3 ubiquitin ligases ubiquitinate target proteins, organism-specific biosystemE3 ubiquitin ligases catalyze the transfer of an ubiquitin from an E2-ubiquitin conjugate to a target protein. Generally, ubiquitin is transferred via formation of an amide bond to a particular lysin...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Parkin-Ubiquitin Proteasomal System pathway, organism-specific biosystem (from WikiPathways)
    Parkin-Ubiquitin Proteasomal System pathway, organism-specific biosystemThis pathway describes the Parkin-Ubiquitin proteasome degradation system.
  • Parkinson's disease, organism-specific biosystem (from KEGG)
    Parkinson's disease, organism-specific biosystemParkinson's disease (PD) is a progressive neurodegenerative movement disorder that results primarily from the death of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNc). Mutations...
  • Parkinsons Disease Pathway, organism-specific biosystem (from WikiPathways)
    Parkinsons Disease Pathway, organism-specific biosystemMost people with Parkinson's disease have idiopathic Parkinson's disease (having no specific known cause). A small proportion of cases, however, can be attributed to known genetic factors. Mutations ...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein ubiquitination, organism-specific biosystem (from REACTOME)
    Protein ubiquitination, organism-specific biosystemUbiquitin is a small, 76 amino acid residue protein that is conjugated by E3 ubiquitin ligases to other proteins in order to regulate their function or degradation (enzymatic cascade reviewed in Neut...
  • Synthesis of active ubiquitin: roles of E1 and E2 enzymes, organism-specific biosystem (from REACTOME)
    Synthesis of active ubiquitin: roles of E1 and E2 enzymes, organism-specific biosystemUbiquitin monomers are processed from larger precursors and then activated by formation of a thiol ester bond between ubiquitin and a cysteine residue of an E1 activating enzyme (UBA1 or UBA6, Jin et...
  • Ubiquitin mediated proteolysis, organism-specific biosystem (from KEGG)
    Ubiquitin mediated proteolysis, organism-specific biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...
  • Ubiquitin mediated proteolysis, conserved biosystem (from KEGG)
    Ubiquitin mediated proteolysis, conserved biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
enzyme binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin conjugating enzyme activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin conjugating enzyme activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin-protein transferase activator activity IGI
Inferred from Genetic Interaction
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-protein transferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-protein transferase activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular protein modification process TAS
Traceable Author Statement
more info
PubMed 
cellular response to glucocorticoid stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to steroid hormone stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein targeting to mitochondrion HMP PubMed 
positive regulation of protein ubiquitination IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of ubiquitin-protein transferase activity IGI
Inferred from Genetic Interaction
more info
PubMed 
protein K11-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein K11-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin ligase complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

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
XP_016884424.1

NCBI Reference Sequences (RefSeq)

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_001256355.1NP_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:67207
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic domain homologues
    COG5078
    Location:67208
    COG5078; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
  2. NM_001256356.1NP_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, DA271653
    Consensus CDS
    CCDS58796.1
    UniProtKB/Swiss-Prot
    P68036
    Related
    ENSP00000445931.1, ENST00000545681.2
    Conserved Domains (1) summary
    pfam00179
    Location:9112
    UQ_con; Ubiquitin-conjugating enzyme
  3. NM_003347.4NP_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
    P68036
    UniProtKB/TrEMBL
    A0A024R1A4
    Related
    ENSP00000344259.4, ENST00000342192.8
    Conserved Domains (1) summary
    smart00212
    Location:6149
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017028935.2XP_016884424.1  ubiquitin-conjugating enzyme E2 L3 isoform X1

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.
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