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

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; 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: mouse all
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Genomic context

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_000022.11 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
UBE2L3 expression in human gastric cancer and its clinical significance.
Title: UBE2L3 expression in human gastric cancer and its clinical significance.
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.
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.
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.
UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus.
Title: UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of hematological and biochemical traits in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiple common variants for celiac disease influencing immune gene expression. EBI GWAS Catalog EBI GWAS CatalogPubMed
New loci associated with chronic hepatitis B virus infection in Han Chinese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Seventy-five genetic loci influencing the human red blood cell. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A004W47 (e-PCR)
- UniSTS:21013

SHGC-172570 (e-PCR)
- UniSTS:183601

A002P29 (e-PCR)
- UniSTS:8526

RH91525 (e-PCR)
- UniSTS:86130

SHGC-80930 (e-PCR)
- UniSTS:102565

REN2036 (e-PCR)
- UniSTS:326836

UBE2L3_3884 (e-PCR)
- UniSTS:463334

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	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 more info	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

EC 2.3.2.23

NP_001243285.1

EC 2.3.2.23

NP_003338.1

EC 2.3.2.23

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_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]
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
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

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
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

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

21549447..21624034

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NM_198157.1: Suppressed sequence

Description

NM_198157.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.