Human Gene NEDD8 (ENST00000250495.10_7) from GENCODE V47lift37
  Description: NEDD8 ubiquitin like modifier (from RefSeq NM_006156.3)
Gencode Transcript: ENST00000250495.10_7
Gencode Gene: ENSG00000129559.13_10
Transcript (Including UTRs)
   Position: hg19 chr14:24,686,063-24,701,573 Size: 15,511 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr14:24,686,333-24,701,473 Size: 15,141 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:24,686,063-24,701,573)mRNA (may differ from genome)Protein (81 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NEDD8_HUMAN
DESCRIPTION: RecName: Full=NEDD8; AltName: Full=Neddylin; AltName: Full=Neural precursor cell expressed developmentally down-regulated protein 8; Short=NEDD-8; AltName: Full=Ubiquitin-like protein Nedd8; Flags: Precursor;
FUNCTION: Ubiquitin-like protein which plays an important role in cell cycle control and embryogenesis. Covalent attachment to its substrates requires prior activation by the E1 complex UBE1C- APPBP1 and linkage to the E2 enzyme UBE2M. Attachment of NEDD8 to cullins activates their associated E3 ubiquitin ligase activity, and thus promotes polyubiquitination and proteasomal degradation of cyclins and other regulatory proteins.
SUBUNIT: Directly interacts with NUB1 and AHR. Covalently attached to cullins and p53.
SUBCELLULAR LOCATION: Nucleus. Note=Mainly nuclear.
TISSUE SPECIFICITY: Highly expressed in heart, skeletal muscle, spleen, thymus, prostate, testis, ovary, colon and leukocytes.
PTM: Cleavage of precursor form by UCHL3 or SENP8 is necessary for function.
SIMILARITY: Belongs to the ubiquitin 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


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

+  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: 1.20 RPKM in Esophagus - Mucosa
Total median expression: 28.77 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 -29.20100-0.292 Picture PostScript Text
3' UTR -75.20270-0.279 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
IPR000626 - Ubiquitin
IPR019954 - Ubiquitin_CS
IPR019956 - Ubiquitin_subgr
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00240 - Ubiquitin family
PF11976 - Ubiquitin-2 like Rad60 SUMO-like
PF13881 - Ubiquitin-2 like Rad60 SUMO-like
PF14560 - Ubiquitin-like domain

SCOP Domains:
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1NDD - X-ray MuPIT 1R4M - X-ray MuPIT 1R4N - X-ray MuPIT 1XT9 - X-ray MuPIT 2BKR - X-ray MuPIT 2KO3 - NMR MuPIT 2NVU - X-ray MuPIT 3DBH - X-ray MuPIT 3DBL - X-ray MuPIT 3DBR - X-ray MuPIT 3DQV - X-ray MuPIT 3GZN - X-ray MuPIT 4F8C - X-ray MuPIT 4FBJ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15843
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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0031625 ubiquitin protein ligase binding

Biological Process:
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006464 cellular protein modification process
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006879 cellular iron ion homeostasis
GO:0008104 protein localization
GO:0009653 anatomical structure morphogenesis
GO:0014070 response to organic cyclic compound
GO:0016579 protein deubiquitination
GO:0043687 post-translational protein modification
GO:0045116 protein neddylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ891688 - Synthetic construct Homo sapiens clone ccsbBroadEn_01082 NEDD8 gene, encodes complete protein.
BC038290 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 8, mRNA (cDNA clone IMAGE:6047397).
BC104664 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 8, mRNA (cDNA clone MGC:104393 IMAGE:6560920), complete cds.
D23662 - Homo sapiens mRNA for ubiquitin-like protein, complete cds.
JD283921 - Sequence 264945 from Patent EP1572962.
JD081904 - Sequence 62928 from Patent EP1572962.
JD224019 - Sequence 205043 from Patent EP1572962.
JD385624 - Sequence 366648 from Patent EP1572962.
JD437701 - Sequence 418725 from Patent EP1572962.
BC104200 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 8, mRNA (cDNA clone MGC:125896 IMAGE:40031350), complete cds.
BC104201 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 8, mRNA (cDNA clone MGC:125897 IMAGE:40031351), complete cds.
JD205933 - Sequence 186957 from Patent EP1572962.
JD442474 - Sequence 423498 from Patent EP1572962.
AB528959 - Synthetic construct DNA, clone: pF1KB6715, Homo sapiens NEDD8 gene for neural precursor cell expressed, developmentally down-regulated 8, without stop codon, in Flexi system.
CR407662 - Homo sapiens full open reading frame cDNA clone RZPDo834G0316D for gene NEDD8, neural precursor cell expressed, developmentally down-regulated 8 complete cds, without stopcodon.
JD488750 - Sequence 469774 from Patent EP1572962.
JD309335 - Sequence 290359 from Patent EP1572962.
JD049300 - Sequence 30324 from Patent EP1572962.
BC064899 - Homo sapiens cDNA clone IMAGE:6008187, partial cds.
JD104393 - Sequence 85417 from Patent EP1572962.
JD176966 - Sequence 157990 from Patent EP1572962.
JD336757 - Sequence 317781 from Patent EP1572962.
JD452886 - Sequence 433910 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q15843 (Reactome details) participates in the following event(s):

R-HSA-5691176 NEDD8 binds CUL1 (in SKP1:CUL1:FXBL5)
R-HSA-8951648 NEDD8 covalently binds catalytic cysteine of UBA3:NAE1
R-HSA-8951656 NEDD8-UBA3:NAE1 binds a second NEDD8
R-HSA-8951644 Release of mature NEDD8
R-HSA-8956040 COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-5690808 UCHL3, SENP8 cleave NEDD8
R-HSA-8956045 COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex
R-HSA-8951751 Doubly neddylated UBA3:NAE1 binds AcM-UBE2M
R-HSA-8951766 Doubly neddylated UBA3:NAE1 binds AcM-UBE2F
R-HSA-8956140 NEDD8 and UBD bind NUB1 and the 26S proteasome
R-HSA-4332236 CBL neddylates TGFBR2
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-8952039 NEDD8:AcM-UBE2F binds CRL5 E3 ubiquitin ligase complex
R-HSA-8951764 Transfer of NEDD8 to AcM-UBE2F
R-HSA-8952639 NEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex
R-HSA-5691108 SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2
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-8952044 AcM-UBE2F transfers NEDD8 to CRL5 E3 ubiquitin ligase complex
R-HSA-8952638 AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex
R-HSA-8956099 VHL:EloB,C:NEDD8-CUL2:RBX1 complex binds UBXN7
R-HSA-8956103 VHL:EloB,C:NEDD8-CUL2:RBX1 complex binds hydroxyprolyl-HIF-alpha
R-HSA-8956050 NEDD8-CUL9:RBX1 binds CUL7:CCDC8:OBSL1
R-HSA-8956106 VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
R-HSA-8956026 CUL9:RBX1 ubiquitinates BIRC5
R-HSA-917937 Iron uptake and transport
R-HSA-8951664 Neddylation
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-5689603 UCH proteinases
R-HSA-382551 Transport of small molecules
R-HSA-597592 Post-translational protein modification
R-HSA-2173789 TGF-beta receptor signaling activates SMADs
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-5688426 Deubiquitination
R-HSA-392499 Metabolism of proteins
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-199991 Membrane Trafficking
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-5653656 Vesicle-mediated transport
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000250495.1, ENST00000250495.2, ENST00000250495.3, ENST00000250495.4, ENST00000250495.5, ENST00000250495.6, ENST00000250495.7, ENST00000250495.8, ENST00000250495.9, NEDD8 , NEDD8_HUMAN, NM_006156, Q15843, Q3SXN8, Q6LES6, uc317fbv.1, uc317fbv.2
UCSC ID: ENST00000250495.10_7
RefSeq Accession: NM_006156.3
Protein: Q15843 (aka NEDD8_HUMAN or NED8_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.