Human Gene UBE2D2 (ENST00000398733.8_8) from GENCODE V47lift37
  Description: ubiquitin conjugating enzyme E2 D2, transcript variant 1 (from RefSeq NM_003339.3)
Gencode Transcript: ENST00000398733.8_8
Gencode Gene: ENSG00000131508.17_14
Transcript (Including UTRs)
   Position: hg19 chr5:138,940,924-139,008,019 Size: 67,096 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr5:138,941,377-139,006,386 Size: 65,010 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:138,940,924-139,008,019)mRNA (may differ from genome)Protein (147 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UB2D2_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin-conjugating enzyme E2 D2; EC=6.3.2.19; AltName: Full=Ubiquitin carrier protein D2; AltName: Full=Ubiquitin-conjugating enzyme E2(17)KB 2; AltName: Full=Ubiquitin-conjugating enzyme E2-17 kDa 2; AltName: Full=Ubiquitin-protein ligase D2;
FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys- 48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP- induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.
CATALYTIC ACTIVITY: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex and with E3 ubiquitin-protein ligase PJA2 (By similarity). Interacts with PDZRN3 (By similarity). Interacts with CNOT4 (via RING domain).
INTERACTION: O15151:MDM4; NbExp=2; IntAct=EBI-347677, EBI-398437; Q96FW1:OTUB1; NbExp=2; IntAct=EBI-347677, EBI-1058491; Q9Y3C5:RNF11; NbExp=4; IntAct=EBI-347677, EBI-396669; Q68DV7:RNF43; NbExp=2; IntAct=EBI-347677, EBI-1647060; Q99942:RNF5; NbExp=3; IntAct=EBI-347677, EBI-348482; Q9Y4K3:TRAF6; NbExp=2; IntAct=EBI-347677, EBI-359276; P98170:XIAP; NbExp=2; IntAct=EBI-347677, EBI-517127; Q8ND25:ZNRF1; NbExp=4; IntAct=EBI-347677, EBI-2129250;
SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: UBE2D2
Diseases sorted by gene-association score: smallpox (3), retinitis pigmentosa 42 (2), retinitis pigmentosa (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 51.49 RPKM in Testis
Total median expression: 1253.93 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -227.30453-0.502 Picture PostScript Text
3' UTR -385.401633-0.236 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1UR6 - NMR 1W4U - NMR MuPIT 2C4O - X-ray 2CLW - X-ray MuPIT 2ESK - X-ray MuPIT 2ESO - X-ray MuPIT 2ESP - X-ray MuPIT 2ESQ - X-ray MuPIT 3A33 - X-ray MuPIT 3JVZ - X-ray MuPIT 3JW0 - X-ray MuPIT 3L1Y - X-ray MuPIT 3TGD - X-ray MuPIT 4A49 - X-ray 4A4B - X-ray MuPIT 4A4C - X-ray MuPIT 4AUQ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P62837
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  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:0000209 protein polyubiquitination
GO:0006464 cellular protein modification process
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006625 protein targeting to peroxisome
GO:0016567 protein ubiquitination
GO:0051865 protein autoubiquitination
GO:0070936 protein K48-linked ubiquitination

Cellular Component:
GO:0000151 ubiquitin ligase complex
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0032991 macromolecular complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC033349 - Homo sapiens ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast), mRNA (cDNA clone MGC:42697 IMAGE:4827210), complete cds.
BC048426 - Homo sapiens ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast), mRNA (cDNA clone IMAGE:4823527).
AK001428 - Homo sapiens cDNA FLJ10566 fis, clone NT2RP2002959, highly similar to Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19).
BC019052 - Homo sapiens ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast), mRNA (cDNA clone IMAGE:4644249).
AK001311 - Homo sapiens cDNA FLJ10449 fis, clone NT2RP1000947, highly similar to Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19).
AY651263 - Homo sapiens ubiquitin-conjugating enzyme E2 D2 transcript variant 1 mRNA, complete cds.
U39317 - Human E2 ubiquitin conjugating enzyme UbcH5B (UBCH5B) mRNA, complete cds.
KJ892342 - Synthetic construct Homo sapiens clone ccsbBroadEn_01736 UBE2D2 gene, encodes complete protein.
AB590980 - Synthetic construct DNA, clone: pFN21AE1630, Homo sapiens UBE2D2 gene for ubiquitin-conjugating enzyme E2D 2, without stop codon, in Flexi system.
AK310273 - Homo sapiens cDNA, FLJ17315.
AF317220 - Homo sapiens ubiquitin-conjugating enzyme (PUBC1) mRNA, complete cds.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7511 - protein ubiquitination

Reactome (by CSHL, EBI, and GO)

Protein P62837 (Reactome details) participates in the following event(s):

R-HSA-1234163 Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha
R-HSA-8953946 PEX2:PEX10:PEX12 monoubiquitinates PEX5S,L at cysteine-11
R-HSA-8956106 VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
R-HSA-9033485 PEX2:PEX10:PEX12 monoubiquitinates PEX5L at cysteine-11
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-1234172 Nuclear VBC complex ubiquitinylates HIF-alpha
R-HSA-8852130 UBA1 conjugates ubiquitin to nuclear E2 enzymes
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-8939323 RNF181 binds BCL10 and Ubiquitin:E2
R-HSA-8953917 PEX2:PEX10:PEX12 binds PEX5S,L (in PEX5S:PEX13:PEX14) and Ub:UBE2D1,2,3
R-HSA-9033527 PEX2:PEX10:PEX12 binds PEX5L (in PEX5L:PEX7:PEX13:PEX14:PEX2:PEX10:PEX12) and Ub:UBE2D1,2,3
R-HSA-168915 K63-linked ubiquitination of RIP1 bound to the activated TLR complex
R-HSA-9014342 K63-linked ubiquitination of RIP1 bound to the activated TLR complex
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-9033241 Peroxisomal protein import
R-HSA-8951664 Neddylation
R-HSA-202424 Downstream TCR signaling
R-HSA-2871837 FCERI mediated NF-kB activation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-HSA-936440 Negative regulators of DDX58/IFIH1 signaling
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-8852135 Protein ubiquitination
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification
R-HSA-202403 TCR signaling
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-168928 DDX58/IFIH1-mediated induction of interferon-alpha/beta
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-2262749 Cellular response to hypoxia
R-HSA-1280218 Adaptive Immune System
R-HSA-168249 Innate Immune System
R-HSA-2262752 Cellular responses to stress
R-HSA-168256 Immune System
R-HSA-937041 IKK complex recruitment mediated by RIP1
R-HSA-168927 TICAM1, RIP1-mediated IKK complex recruitment
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-937061 TRIF(TICAM1)-mediated TLR4 signaling
R-HSA-168164 Toll Like Receptor 3 (TLR3) Cascade
R-HSA-166166 MyD88-independent TLR4 cascade
R-HSA-168898 Toll-Like Receptors Cascades
R-HSA-166016 Toll Like Receptor 4 (TLR4) Cascade

-  Other Names for This Gene
  Alternate Gene Symbols: D3DQC9, ENST00000398733.1, ENST00000398733.2, ENST00000398733.3, ENST00000398733.4, ENST00000398733.5, ENST00000398733.6, ENST00000398733.7, NM_003339, P51669, P62837, PUBC1, Q3MN78, Q96RP6, UB2D2_HUMAN, UBC4, UBC5B, UBCH4, UBCH5B, uc318zxg.1, uc318zxg.2
UCSC ID: ENST00000398733.8_8
RefSeq Accession: NM_003339.3
Protein: P62837 (aka UB2D2_HUMAN or UB5B_HUMAN)

-  Gene Model Information
  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.