Human Gene UBE4B (ENST00000253251.12) from GENCODE V38
  Description: Homo sapiens ubiquitination factor E4B (UBE4B), transcript variant 2, mRNA. (from RefSeq NM_006048)
RefSeq Summary (NM_006048): 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 an additional conjugation factor, E4, which is involved in multiubiquitin chain assembly. This gene is also the strongest candidate in the neuroblastoma tumor suppressor genes. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000253251.12
Gencode Gene: ENSG00000130939.20
Transcript (Including UTRs)
   Position: hg38 chr1:10,032,832-10,180,367 Size: 147,536 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg38 chr1:10,033,671-10,179,956 Size: 146,286 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:10,032,832-10,180,367)mRNA (may differ from genome)Protein (1173 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ubiquitin conjugation factor E4 B; AltName: Full=Homozygously deleted in neuroblastoma 1; AltName: Full=Ubiquitin fusion degradation protein 2;
FUNCTION: Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity).
SUBUNIT: Interacts with VCP (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
TISSUE SPECIFICITY: Highest expression in ovary, testis, heart and skeletal muscle. Expression is low in colon, thymus and peripheral blood leukocytes. Almost undetectable in lung and spleen.
PTM: Proteolytically cleaved by caspases during apoptosis. Cleaved efficiently at Asp-123 by caspase-6 and granzyme B. Cleaved with approximately 10-fold less efficiency at Asp-109 by caspase-3 and caspase-7.
SIMILARITY: Belongs to the ubiquitin conjugation factor E4 family.
SIMILARITY: Contains 1 U-box domain.
SEQUENCE CAUTION: Sequence=BAA31659.3; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: UBE4B
Diseases sorted by gene-association score: neuroblastoma (6), deafness, autosomal dominant 25 (2), wallerian degeneration (2)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.40 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 528.28 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 -367.60839-0.438 Picture PostScript Text
3' UTR -119.50411-0.291 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
IPR019474 - Ub_conjug_fac_E4_core
IPR003613 - Ubox_domain

Pfam Domains:
PF04564 - U-box domain
PF10408 - Ubiquitin elongating factor core

Protein Data Bank (PDB) 3-D Structure
MuPIT help


- X-ray MuPIT

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on O95155
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
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsemblEnsembl SGD
Protein SequenceProtein Sequence Protein Sequence Protein Sequence
AlignmentAlignment Alignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0019899 enzyme binding
GO:0034450 ubiquitin-ubiquitin ligase activity
GO:0051117 ATPase binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0003222 ventricular trabecula myocardium morphogenesis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006513 protein monoubiquitination
GO:0008626 granzyme-mediated apoptotic signaling pathway
GO:0009411 response to UV
GO:0016567 protein ubiquitination
GO:0030433 ER-associated ubiquitin-dependent protein catabolic process
GO:0031175 neuron projection development
GO:0034976 response to endoplasmic reticulum stress
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0044257 cellular protein catabolic process
GO:0051865 protein autoubiquitination

Cellular Component:
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005737 cytoplasm

-  Descriptions from all associated GenBank mRNAs
  AB028839 - Homo sapiens HDNB1(homzygously deleted in neuroblastoma-1)/UFD2 mRNA, complete cds.
LF383929 - JP 2014500723-A/191432: Polycomb-Associated Non-Coding RNAs.
MA619506 - JP 2018138019-A/191432: Polycomb-Associated Non-Coding RNAs.
AB014584 - Homo sapiens KIAA0684 mRNA for KIAA0684 protein.
AK292444 - Homo sapiens cDNA FLJ78424 complete cds, highly similar to Homo sapiens ubiquitination factor E4B (UFD2 homolog, yeast) (UBE4B), mRNA.
BC047890 - Homo sapiens ubiquitination factor E4B (UFD2 homolog, yeast), mRNA (cDNA clone IMAGE:5492405), containing frame-shift errors.
BC093696 - Homo sapiens ubiquitination factor E4B (UFD2 homolog, yeast), mRNA (cDNA clone MGC:120731 IMAGE:7939541), complete cds.
BC143458 - Homo sapiens cDNA clone IMAGE:9051966.
BC143460 - Homo sapiens cDNA clone IMAGE:9051968.
AF043117 - Homo sapiens ubiquitin-fusion degradation protein 2 (UFD2) mRNA, complete cds.
AF331520 - Homo sapiens ubiquitin-fusion degradation protein 2 mRNA, complete cds.
JF289274 - Homo sapiens Ufd2a-III/UBE4B-III splice isoform (Ube4B) mRNA, complete cds, alternatively spliced.
LF206732 - JP 2014500723-A/14235: Polycomb-Associated Non-Coding RNAs.
MA442309 - JP 2018138019-A/14235: Polycomb-Associated Non-Coding RNAs.
LF357423 - JP 2014500723-A/164926: Polycomb-Associated Non-Coding RNAs.
MA593000 - JP 2018138019-A/164926: Polycomb-Associated Non-Coding RNAs.
LF357421 - JP 2014500723-A/164924: Polycomb-Associated Non-Coding RNAs.
MA592998 - JP 2018138019-A/164924: Polycomb-Associated Non-Coding RNAs.
AK304484 - Homo sapiens cDNA FLJ50370 complete cds, highly similar to Ubiquitin conjugation factor E4 B.
AK023654 - Homo sapiens cDNA FLJ13592 fis, clone PLACE1009477, highly similar to Homo sapiens ubiquitin-fusion degradation protein 2 (UFD2) mRNA.
AF091093 - Homo sapiens clone 686 unknown mRNA, complete sequence.
LF357418 - JP 2014500723-A/164921: Polycomb-Associated Non-Coding RNAs.
MA592995 - JP 2018138019-A/164921: Polycomb-Associated Non-Coding RNAs.
LF357417 - JP 2014500723-A/164920: Polycomb-Associated Non-Coding RNAs.
MA592994 - JP 2018138019-A/164920: Polycomb-Associated Non-Coding RNAs.
JD128952 - Sequence 109976 from Patent EP1572962.
JD473236 - Sequence 454260 from Patent EP1572962.
JD449846 - Sequence 430870 from Patent EP1572962.

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

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000253251.1, ENST00000253251.10, ENST00000253251.11, ENST00000253251.2, ENST00000253251.3, ENST00000253251.4, ENST00000253251.5, ENST00000253251.6, ENST00000253251.7, ENST00000253251.8, ENST00000253251.9, HDNB1, KIAA0684, NM_006048, O75169, O95155, O95338, Q5SZ12, Q5SZ16, Q96QD4, Q9BYI7, UBE4B_HUMAN, uc001aqr.1, uc001aqr.2, uc001aqr.3, uc001aqr.4, uc001aqr.5, UFD2
UCSC ID: ENST00000253251.12
RefSeq Accession: NM_006048
Protein: O95155 (aka UBE4B_HUMAN or UB4B_HUMAN)

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