Human Gene UBE2M (ENST00000253023.8_7) from GENCODE V47lift37
  Description: ubiquitin conjugating enzyme E2 M (from RefSeq NM_003969.4)
Gencode Transcript: ENST00000253023.8_7
Gencode Gene: ENSG00000130725.8_14
Transcript (Including UTRs)
   Position: hg19 chr19:59,067,079-59,069,978 Size: 2,900 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr19:59,067,456-59,069,748 Size: 2,293 Coding Exon Count: 6 

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 (chr19:59,067,079-59,069,978)mRNA (may differ from genome)Protein (183 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBC12_HUMAN
DESCRIPTION: RecName: Full=NEDD8-conjugating enzyme Ubc12; EC=6.3.2.-; AltName: Full=NEDD8 carrier protein; AltName: Full=NEDD8 protein ligase; AltName: Full=Ubiquitin-conjugating enzyme E2 M;
FUNCTION: Accepts the ubiquitin-like protein NEDD8 from the UBA3- NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The specific interaction with the E3 ubiquitin ligase RBX1, but not RBX2, suggests that the RBX1-UBE2M complex neddylates specific target proteins, such as CUL1, CUL2, CUL3 and CUL4. Involved in cell proliferation.
CATALYTIC ACTIVITY: ATP + NEDD8 + protein lysine = AMP + diphosphate + protein N-NEDD8yllysine.
PATHWAY: Protein modification; protein neddylation.
SUBUNIT: Interacts with UBA3, DCUN1D1 and RBX1.
INTERACTION: Q8TBC4:UBA3; NbExp=2; IntAct=EBI-1041660, EBI-717567;
DOMAIN: Both the N-terminal docking peptide and the catalytic core domain must bind the UBA3-NAE1 complex simultaneously for optimal transfer of NEDD8.
PTM: The acetylation of Met-1 is cotranslational, and not regulatory. The N-acetylmethionine increases affinity for DCUN1D1 by about 2 orders of magnitude and is crucial for NEDD8 transfer to cullins.
SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family. UBC12 subfamily.

-  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: UBE2M
Diseases sorted by gene-association score: familial hypertension (2)

-  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: 77.24 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 1780.50 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 -134.80230-0.586 Picture PostScript Text
3' UTR -175.90377-0.467 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
1TT5 - X-ray MuPIT 1Y8X - X-ray MuPIT 2NVU - X-ray MuPIT 3TDU - X-ray MuPIT 3TDZ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P61081
FrontTopSide
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 orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  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:0019788 NEDD8 transferase activity
GO:0031625 ubiquitin protein ligase binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0006464 cellular protein modification process
GO:0016567 protein ubiquitination
GO:0043525 positive regulation of neuron apoptotic process
GO:0043687 post-translational protein modification
GO:0045116 protein neddylation

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


-  Descriptions from all associated GenBank mRNAs
  BC058924 - Homo sapiens ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast), mRNA (cDNA clone MGC:65116 IMAGE:6162220), complete cds.
GQ891447 - Homo sapiens clone HEL-S-168 epididymis secretory sperm binding protein mRNA, complete cds.
BC007657 - Homo sapiens cDNA clone IMAGE:3344837, **** WARNING: chimeric clone ****.
AF075599 - Homo sapiens ubiquitin conjugating enzyme 12 (UBC12) mRNA, complete cds.
JD040795 - Sequence 21819 from Patent EP1572962.
JD025709 - Sequence 6733 from Patent EP1572962.
JD028202 - Sequence 9226 from Patent EP1572962.
JD541784 - Sequence 522808 from Patent EP1572962.
JD403307 - Sequence 384331 from Patent EP1572962.
JD541783 - Sequence 522807 from Patent EP1572962.
JD560828 - Sequence 541852 from Patent EP1572962.
JD405131 - Sequence 386155 from Patent EP1572962.
AB012191 - Homo sapiens mRNA for Nedd8-conjugating enzyme hUbc12, complete cds.
BT006754 - Homo sapiens ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast) mRNA, complete cds.
CU691336 - Synthetic construct Homo sapiens gateway clone IMAGE:100021592 5' read UBE2M mRNA.
KJ892674 - Synthetic construct Homo sapiens clone ccsbBroadEn_02068 UBE2M gene, encodes complete protein.
AB590888 - Synthetic construct DNA, clone: pFN21AE1664, Homo sapiens UBE2M gene for ubiquitin-conjugating enzyme E2M, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7899 - protein NEDDylation

BioCarta from NCI Cancer Genome Anatomy Project
h_p27Pathway - Regulation of p27 Phosphorylation during Cell Cycle Progression

Reactome (by CSHL, EBI, and GO)

Protein P61081 (Reactome details) participates in the following event(s):

R-HSA-8951751 Doubly neddylated UBA3:NAE1 binds AcM-UBE2M
R-HSA-4332236 CBL neddylates TGFBR2
R-HSA-8952618 AcM-UBE2M transfers NEDD8 to CRL1 E3 ubiquitin ligase complex
R-HSA-8956025 AcM-UBE2M transfers NEDD8 to CUL9:RBX1
R-HSA-8952638 AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex
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-8952620 NEDD8:AcM-UBE2M binds CRL1 E3 ubiquitin ligase complex
R-HSA-8956031 NEDD8:AcM-UBE2M binds CUL9:RBX1 ubiquitin ligase complex
R-HSA-8951661 Transfer of NEDD8 to AcM-UBE2M
R-HSA-8952639 NEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-HSA-5676590 NIK-->noncanonical NF-kB signaling
R-HSA-8951664 Neddylation
R-HSA-2173789 TGF-beta receptor signaling activates SMADs
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-597592 Post-translational protein modification
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-392499 Metabolism of proteins
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-1280218 Adaptive Immune System
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000253023.1, ENST00000253023.2, ENST00000253023.3, ENST00000253023.4, ENST00000253023.5, ENST00000253023.6, ENST00000253023.7, NM_003969, O76069, P61081, Q8VC50, UBC12, UBC12_HUMAN, uc317fjr.1, uc317fjr.2
UCSC ID: ENST00000253023.8_7
RefSeq Accession: NM_003969.4
Protein: P61081 (aka UBC12_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.