Human Gene UBE2E3 (uc002unr.1) Description and Page Index
  Description: Homo sapiens ubiquitin-conjugating enzyme E2E 3 (UBE2E3), transcript variant 1, mRNA.
RefSeq Summary (NM_006357): 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. The encoded protein shares 100% sequence identity with the mouse and rat counterparts, which indicates that this enzyme is highly conserved in eukaryotes. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jun 2013].
Transcript (Including UTRs)
   Position: hg19 chr2:181,845,342-181,928,150 Size: 82,809 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr2:181,846,770-181,927,615 Size: 80,846 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:181,845,342-181,928,150)mRNA (may differ from genome)Protein (207 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ubiquitin-conjugating enzyme E2 E3; EC=; AltName: Full=UbcH9; AltName: Full=Ubiquitin carrier protein E3; AltName: Full=Ubiquitin-conjugating enzyme E2-23 kDa; AltName: Full=Ubiquitin-protein ligase E3;
FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys- 11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination. Participates in the regulation of transepithelial sodium transport in renal cells. May be involved in cell growth arrest.
CATALYTIC ACTIVITY: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: The ubiquitin-loaded form interacts specifically with importin-11 (IPO11), leading to its import into the nucleus (By similarity). Interacts with NEDD4L.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Shuttles between the nucleus and cytoplasm in a IPO11-dependent manner.
TISSUE SPECIFICITY: Ubiquitously expressed at low levels. Highly expressed in skeletal muscle.
SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): UBE2E3
CDC HuGE Published Literature: UBE2E3
Positive Disease Associations: Celiac disease , Heart Function Tests , Spondylitis, Ankylosing
Related Studies:
  1. Celiac disease
    Dubois ,et al. Nat Genet 2010, Multiple common variants for celiac disease influencing immune gene expression , Nature genetics 2010 42- 4 : 295-302. [PubMed 20190752]
  2. Celiac Disease
    Patrick C A Dubois et al. Nature genetics 2010, Multiple common variants for celiac disease influencing immune gene expression., Nature genetics. [PubMed 20190752]
  3. Heart Function Tests
    Joshua C Denny et al. Circulation 2010, Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science., Circulation. [PubMed 21041692]
    This genome-wide association study confirms a gene heretofore not implicated in cardiac pathophysiology as a modulator of PR interval in humans. This study is one of the first replication genome-wide association studies performed with the use of an electronic medical records-derived cohort, supporting their further use for genotype-phenotype analyses.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.73 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1021.98 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -156.82384-0.408 Picture PostScript Text
3' UTR -132.30535-0.247 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000608 - UBQ-conjugat_E2
IPR023313 - UBQ-conjugating_AS
IPR016135 - UBQ-conjugating_enzyme/RWD

Pfam Domains:
PF00179 - Ubiquitin-conjugating enzyme

SCOP Domains:
54495 - UBC-like

ModBase Predicted Comparative 3D Structure on Q969T4
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0061631 ubiquitin conjugating enzyme activity

Biological Process:
GO:0016567 protein ubiquitination
GO:0040008 regulation of growth
GO:0070534 protein K63-linked ubiquitination
GO:0070936 protein K48-linked ubiquitination
GO:0070979 protein K11-linked ubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol

-  Descriptions from all associated GenBank mRNAs
  KJ893054 - Synthetic construct Homo sapiens clone ccsbBroadEn_02448 UBE2E3 gene, encodes complete protein.
LF383701 - JP 2014500723-A/191204: Polycomb-Associated Non-Coding RNAs.
BC092407 - Homo sapiens ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast), mRNA (cDNA clone MGC:102809 IMAGE:6180242), complete cds.
AF085362 - Homo sapiens UbcM2 mRNA, complete cds.
BC003554 - Homo sapiens ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast), mRNA (cDNA clone MGC:1316 IMAGE:3537280), complete cds.
AB017644 - Homo sapiens UbcH9 mRNA for ubiquitin-conjugating enzyme E2, complete cds.
BC003687 - Homo sapiens ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast), mRNA (cDNA clone IMAGE:3453243).
MA619278 - JP 2018138019-A/191204: Polycomb-Associated Non-Coding RNAs.
JD121394 - Sequence 102418 from Patent EP1572962.
JD115065 - Sequence 96089 from Patent EP1572962.
JD195739 - Sequence 176763 from Patent EP1572962.
AK314145 - Homo sapiens cDNA, FLJ94847, Homo sapiens ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast) (UBE2E3), mRNA.
LF347616 - JP 2014500723-A/155119: Polycomb-Associated Non-Coding RNAs.
AB528700 - Synthetic construct DNA, clone: pF1KB6933, Homo sapiens UBE2E3 gene for ubiquitin-conjugating enzyme E2E 3, without stop codon, in Flexi system.
BT019345 - Homo sapiens ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast) mRNA, complete cds.
LF347617 - JP 2014500723-A/155120: Polycomb-Associated Non-Coding RNAs.
JD339731 - Sequence 320755 from Patent EP1572962.
JD102770 - Sequence 83794 from Patent EP1572962.
JD241139 - Sequence 222163 from Patent EP1572962.
JD183632 - Sequence 164656 from Patent EP1572962.
JD433065 - Sequence 414089 from Patent EP1572962.
MA583193 - JP 2018138019-A/155119: Polycomb-Associated Non-Coding RNAs.
MA583194 - JP 2018138019-A/155120: Polycomb-Associated Non-Coding RNAs.
LF347633 - JP 2014500723-A/155136: Polycomb-Associated Non-Coding RNAs.
LF347634 - JP 2014500723-A/155137: Polycomb-Associated Non-Coding RNAs.
JD295505 - Sequence 276529 from Patent EP1572962.
MA583210 - JP 2018138019-A/155136: Polycomb-Associated Non-Coding RNAs.
MA583211 - JP 2018138019-A/155137: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04120 - Ubiquitin mediated proteolysis

Reactome (by CSHL, EBI, and GO)

Protein Q969T4 (Reactome details) participates in the following event(s):

R-HSA-8852127 UBA6 conjugates ubiquitin to cytosolic E2 enzymes
R-HSA-8852129 UBA1 conjugates ubiquitin to cytosolic E2 enzymes
R-HSA-983152 Transfer of ubiquitin from E1 to E2
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-8852130 UBA1 conjugates ubiquitin to nuclear E2 enzymes
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-8852135 Protein ubiquitination
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-597592 Post-translational protein modification
R-HSA-1280218 Adaptive Immune System
R-HSA-392499 Metabolism of proteins
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAD6, D3DPG3, NM_006357, NP_872619, Q5U0R7, Q7Z4W4, Q969T4, UB2E3_HUMAN, UBCE4, UBCH9
UCSC ID: uc002unr.1
RefSeq Accession: NM_006357
Protein: Q969T4 (aka UB2E3_HUMAN or UB6C_HUMAN)
CCDS: CCDS2282.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_006357.2
exon count: 6CDS single in 3' UTR: no RNA size: 1559
ORF size: 624CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1361.00frame shift in genome: no % Coverage: 98.97
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 327# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.