UBE2D3 ubiquitin conjugating enzyme E2 D3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UBE2D3provided by HGNC
Official Full Name: ubiquitin conjugating enzyme E2 D3provided by HGNC
Primary source: HGNC:HGNC:12476
See related: Ensembl:ENSG00000109332 MIM:602963; AllianceGenome:HGNC:12476
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: UBC4/5; UBCH5C; E2(17)KB3
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. This enzyme functions in the ubiquitination of the tumor-suppressor protein p53, which is induced by an E3 ubiquitin-protein ligase. [provided by RefSeq, Jan 2017]
Expression: Ubiquitous expression in bone marrow (RPKM 59.8), thyroid (RPKM 40.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q24

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (102794383..102868895, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (106108341..106183222, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (103715540..103790052, complement)

Chromosome 4 - NC_000004.12 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
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?

Ubiquitinome Profiling Reveals in Vivo UBE2D3 Targets and Implicates UBE2D3 in Protein Quality Control.
Title: Ubiquitinome Profiling Reveals in Vivo UBE2D3 Targets and Implicates UBE2D3 in Protein Quality Control.
UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma.
Title: UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma.
Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3.
Title: Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3.
UbcH5 Interacts with Substrates to Participate in Lysine Selection with the E3 Ubiquitin Ligase CHIP.
Title: UbcH5 Interacts with Substrates to Participate in Lysine Selection with the E3 Ubiquitin Ligase CHIP.
Together with Riplet, Ube2D3 promotes covalent conjugation of polyubiquitin chains to RIG-I, while Ube2N preferentially facilitates production of unanchored chains. In the presence of these chains, RIG-I induces MAVS aggregation directly on the mitochondria. Data thus reveal two essential mechanisms underlying the activation of RIG-I and MAVS for triggering innate immune signaling in response to viral infection in cells.
Title: Ube2D3 and Ube2N are essential for RIG-I-mediated MAVS aggregation in antiviral innate immunity.
Findings indicate that UBE2D3 enhances radiosensitivity of EC109 cells by degradating hTERT through the ubiquitin proteolysis pathway.
Title: UBE2D3 gene overexpression increases radiosensitivity of EC109 esophageal cancer cells in vitro and in vivo.
Data show that ubiquitin E2 enzymes UBE2D1/2/3 and E3 ligase RNF138 accumulate at DNA-damage sites and act at early resection stages by promoting CtIP protein ubiquitylation and accrual.
Title: Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair.
This study demonistrated by Gene expression profile that UBE3D3 upregulaion in fibroblasts of Huntington's disease patients.
Title: Gene expression profile in fibroblasts of Huntington's disease patients and controls.
These data reveal novel insights into the Otub1 inhibition of E2 wherein monoubiquitination promotes the interaction of Otub1 with UbcH5 and the function to suppress it.
Title: Monoubiquitination is critical for ovarian tumor domain-containing ubiquitin aldehyde binding protein 1 (Otub1) to suppress UbcH5 enzyme and stabilize p53 protein.
UbcH5c~Ubiqitin binding stabilizes an active conformation of the Shigella flexneri OspG kinase, greatly enhancing its activity.
Title: E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-67354 (e-PCR)
- UniSTS:83968

G19979 (e-PCR)
- UniSTS:35899

SHGC-67632 (e-PCR)
- UniSTS:7997

D4S1572 (e-PCR), detects polymorphism
- UniSTS:11838

RH16693 (e-PCR)
- UniSTS:84034

SHGC-67367 (e-PCR)
- UniSTS:69478

SHGC-37168 (e-PCR)
- UniSTS:62357

SHGC-14304 (e-PCR)
- UniSTS:66966

STS-H95079 (e-PCR)
- UniSTS:6572

AFM265va9 (e-PCR), detects polymorphism
- UniSTS:84175

RH125441 (e-PCR)
- UniSTS:162261

SHGC-25108 (e-PCR)
- UniSTS:17121

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 conjugating enzyme activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of BMP signaling pathway	TAS Traceable Author Statement more info
involved_in negative regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info
involved_in positive regulation of protein targeting to mitochondrion	HMP more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay 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 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 K6-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein modification process	TAS Traceable Author Statement more info	PubMed
involved_in protein monoubiquitination	IDA Inferred from Direct Assay 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 ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin-conjugating enzyme E2 D3

Names: (E3-independent) E2 ubiquitin-conjugating enzyme D3; E2 ubiquitin-conjugating enzyme D3; ubiquitin carrier protein D3; ubiquitin conjugating enzyme E2D 3; ubiquitin-conjugating enzyme E2(17)KB 3; ubiquitin-conjugating enzyme E2-17 kDa 3; ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast); ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5); ubiquitin-protein ligase D3

NP_001287724.1

EC 2.3.2.23

EC 2.3.2.24

NP_003331.1

EC 2.3.2.23

EC 2.3.2.24

NP_871615.1

EC 2.3.2.23

EC 2.3.2.24

NP_871616.1

EC 2.3.2.23

EC 2.3.2.24

NP_871617.1

EC 2.3.2.23

EC 2.3.2.24

NP_871618.1

EC 2.3.2.23

EC 2.3.2.24

NP_871619.1

EC 2.3.2.23

EC 2.3.2.24

NP_871620.1

EC 2.3.2.23

EC 2.3.2.24

NP_871621.1

EC 2.3.2.23

EC 2.3.2.24

NP_871622.1

EC 2.3.2.23

EC 2.3.2.24

XP_024309970.1

EC 2.3.2.23

EC 2.3.2.24

XP_054206763.1

EC 2.3.2.23

EC 2.3.2.24

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_001300795.2 → NP_001287724.1 ubiquitin-conjugating enzyme E2 D3 isoform 4

See identical proteins and their annotated locations for NP_001287724.1

Status: REVIEWED

Description

Transcript Variant: This variant (10) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC018797, AI651378, AK127304, BQ719030, BU677139, CD242548, DA550074, DB234695

Consensus CDS

CCDS75172.1

UniProtKB/TrEMBL

D6RAH7, D6RFM0

Related

ENSP00000424359.1, ENST00000507845.5

Conserved Domains (1) summary

cl00154
Location:1 → 117

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_003340.6 → NP_003331.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_003331.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the predominant isoform (1).

Source sequence(s)

AC018797, BC003395, BM750658, BM967209, DA557036

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000378280.4, ENST00000394801.8

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181886.3 → NP_871615.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_871615.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an additional segment in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC018797, BC003395, BM750658, BM788287, BM967209

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000378283.2, ENST00000394804.6

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181887.3 → NP_871616.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_871616.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC018797, BM967209, DA588940, U39318

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000318494.7, ENST00000321805.11

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181888.3 → NP_871617.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_871617.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks a segment in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC018797, BC003395, BM750658, BM967209, DA335600

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000344069.8, ENST00000349311.12

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181889.2 → NP_871618.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_871618.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) has an alternate 5' UTR exon, and encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC018797, AK315775, BC003395, BM967209, HY035067

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000378282.5, ENST00000394803.9

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181890.3 → NP_871619.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_871619.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) has an alternate 5' UTR exon, and encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC018797, BC003395, BM967209, HY109217

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000337208.3, ENST00000338145.7

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181891.3 → NP_871620.1 ubiquitin-conjugating enzyme E2 D3 isoform 1

See identical proteins and their annotated locations for NP_871620.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) has an additional segment in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC018797, BC003395, BM967209, DA494746

Consensus CDS

CCDS3660.1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000396901.2, ENST00000453744.7

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181892.4 → NP_871621.1 ubiquitin-conjugating enzyme E2 D3 isoform 2

See identical proteins and their annotated locations for NP_871621.1

Status: REVIEWED

Description

Transcript Variant: This variant (8) differs in the 5' UTR and has an additional exon in the 3' region, as compared to variant 1. It encodes isoform 2, which has a distinct and one aa longer C-terminus, as compared to isoform 1.

Source sequence(s)

AC018797, AK095822, BM967209

Consensus CDS

CCDS3661.1

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000345285.5, ENST00000343106.9

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
NM_181893.3 → NP_871622.1 ubiquitin-conjugating enzyme E2 D3 isoform 3

See identical proteins and their annotated locations for NP_871622.1

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks two consecutive 5' exons, but has an alternate 5' exon, which contains an upstream in-frame start codon, as compared to variant 1. It encodes isoform 3, which has a distinct and two aa longer N-terminus, as compared to isoform 1.

Source sequence(s)

AC018797, BM967209, DA965437, HY109217

Consensus CDS

CCDS3659.1

UniProtKB/TrEMBL

A0A087WY85

Related

ENSP00000349722.6, ENST00000357194.10

Conserved Domains (1) summary

cl00154
Location:6 → 148

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...

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_000004.12 Reference GRCh38.p14 Primary Assembly

Range

102794383..102868895 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024454202.2 → XP_024309970.1 ubiquitin-conjugating enzyme E2 D3 isoform X1

UniProtKB/Swiss-Prot

A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924

UniProtKB/TrEMBL

A0A087WY85

Conserved Domains (1) summary

cl00154
Location:1 → 146

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...