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UBE2D2 ubiquitin conjugating enzyme E2 D2 [ Homo sapiens (human) ]

Gene ID: 7322, updated on 1-Jun-2020

Summary

Official Symbol
UBE2D2provided by HGNC
Official Full Name
ubiquitin conjugating enzyme E2 D2provided by HGNC
Primary source
HGNC:HGNC:12475
See related
Ensembl:ENSG00000131508 MIM:602962
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; PUBC1; UBCH4; UBC4/5; UBCH5B; E2(17)KB2
Summary
Regulated degradation of misfolded, damaged or short-lived proteins in eukaryotes occurs via the ubiquitin (Ub)-proteasome system (UPS). An integral part of the UPS system is the ubiquitination of target proteins and covalent linkage of Ub-containing proteins to form polymeric chains, marking them as targets for 26S proteasome-mediated degradation. Ubiquitination of proteins is mediated by a cascade of enzymes which includes E1 (ubiquitin activating), E2 (ubiquitin conjugating), and E3 (ubiquitin ligases) enzymes. This gene encodes a member of the E2 enzyme family. Substrates of this enzyme include the tumor suppressor protein p53 and peroxisomal biogenesis factor 5 (PEX5). Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]
Expression
Ubiquitous expression in testis (RPKM 32.5), brain (RPKM 24.1) and 25 other tissues See more
Orthologs

Genomic context

See UBE2D2 in Genome Data Viewer
Location:
5q31.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (139561166..139628434)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138940751..139008019)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cancer-related nucleoside-triphosphatase pseudogene Neighboring gene nuclear receptor coactivator 4 pseudogene 4 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 15 Neighboring gene H3 histone pseudogene 25 Neighboring gene CRISPRi-validated cis-regulatory element chr5.3240 Neighboring gene CXXC5 antisense RNA 1 Neighboring gene CXXC finger protein 5

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
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif CUL5/RBX2/ELOB/ELOC/Vif/CBF-beta complex catalyzes polyubiquitin chain formation on A3G in the presence of ubiquitin E2 UBE2R1 (CDC34) or UBCH5b (UBE2D2) PubMed
integrase gag-pol Analysis of HIV-1 proviral integration sites in antiretroviral treatment patients indicates that UBE2D2 gene favors HIV-1 integration for expansion and persistence of infected cells, suggesting HIV-1 IN interacts with UBE2D2 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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
 
protein binding IPI
Inferred from Physical Interaction
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 transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
MyD88-independent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
TRIF-dependent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
cellular protein modification process TAS
Traceable Author Statement
more info
PubMed 
protein K48-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein autoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein targeting to peroxisome TAS
Traceable Author Statement
more info
 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
ubiquitin-conjugating enzyme E2 D2
Names
(E3-independent) E2 ubiquitin-conjugating enzyme D2
E2 ubiquitin-conjugating enzyme D2
p53-regulated ubiquitin-conjugating enzyme 1
ubiquitin carrier protein D2
ubiquitin conjugating enzyme E2D 2
ubiquitin-conjugating enzyme E2-17 kDa 2
ubiquitin-conjugating enzyme E2D 2 (homologous to yeast UBC4/5)
ubiquitin-protein ligase D2
NP_003330.1
NP_862821.1
XP_016865309.1

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_003339.3NP_003330.1  ubiquitin-conjugating enzyme E2 D2 isoform 1

    See identical proteins and their annotated locations for NP_003330.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF317220, AK001311, AK001428, BC033349
    Consensus CDS
    CCDS43369.1
    UniProtKB/Swiss-Prot
    P62837
    Related
    ENSP00000381717.3, ENST00000398733.8
    Conserved Domains (1) summary
    cl00154
    Location:1146
    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 ...
  2. NM_181838.1NP_862821.1  ubiquitin-conjugating enzyme E2 D2 isoform 2

    See identical proteins and their annotated locations for NP_862821.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' region, differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 2 which is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AF317220, AK001311, AK001428, BC033349, BC048426, BQ186099
    Consensus CDS
    CCDS47275.1
    UniProtKB/Swiss-Prot
    P62837
    Related
    ENSP00000424941.1, ENST00000505548.5
    Conserved Domains (1) summary
    cl00154
    Location:1117
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    139561166..139628434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009820.1XP_016865309.1  ubiquitin-conjugating enzyme E2 D2 isoform X1

    Conserved Domains (2) summary
    COG5078
    Location:35173
    COG5078; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
    cl00154
    Location:35172
    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 ...
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