Human Gene UBE4B (ENST00000343090.11_4) from GENCODE V47lift37
  Description: ubiquitination factor E4B, transcript variant 1 (from RefSeq NM_001105562.3)
Gencode Transcript: ENST00000343090.11_4
Gencode Gene: ENSG00000130939.20_11
Transcript (Including UTRs)
   Position: hg19 chr1:10,093,016-10,241,297 Size: 148,282 Total Exon Count: 28 Strand: +
Coding Region
   Position: hg19 chr1:10,093,729-10,240,014 Size: 146,286 Coding Exon Count: 28 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:10,093,016-10,241,297)mRNA (may differ from genome)Protein (1302 aa)
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-  Comments and Description Text from UniProtKB
  ID: UBE4B_HUMAN
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;

-  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: 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

+  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: 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 -292.30713-0.410 Picture PostScript Text
3' UTR -339.701283-0.265 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
IPR013083 - Znf_RING/FYVE/PHD

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

SCOP Domains:
48371 - ARM repeat
57850 - RING/U-box

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2KRE - NMR MuPIT 3L1X - X-ray MuPIT 3L1Z - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95155
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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 DetailsGene Details    
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-  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
  LF206732 - JP 2014500723-A/14235: Polycomb-Associated Non-Coding RNAs.
AB028839 - Homo sapiens HDNB1(homzygously deleted in neuroblastoma-1)/UFD2 mRNA, complete cds.
LF383929 - JP 2014500723-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.
AK304484 - Homo sapiens cDNA FLJ50370 complete cds, highly similar to Ubiquitin conjugation factor E4 B.
MA619506 - JP 2018138019-A/191432: 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.
LF357421 - JP 2014500723-A/164924: Polycomb-Associated Non-Coding RNAs.
AK023654 - Homo sapiens cDNA FLJ13592 fis, clone PLACE1009477, highly similar to Homo sapiens ubiquitin-fusion degradation protein 2 (UFD2) mRNA.
MA593000 - JP 2018138019-A/164926: Polycomb-Associated Non-Coding RNAs.
MA592998 - JP 2018138019-A/164924: Polycomb-Associated Non-Coding RNAs.
AF091093 - Homo sapiens clone 686 unknown mRNA, complete sequence.
LF357418 - JP 2014500723-A/164921: Polycomb-Associated Non-Coding RNAs.
LF357417 - JP 2014500723-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.
JD082320 - Sequence 63344 from Patent EP1572962.
JD232926 - Sequence 213950 from Patent EP1572962.
JD560814 - Sequence 541838 from Patent EP1572962.
JD396363 - Sequence 377387 from Patent EP1572962.
JD235416 - Sequence 216440 from Patent EP1572962.
JD094626 - Sequence 75650 from Patent EP1572962.
JD554995 - Sequence 536019 from Patent EP1572962.
MA592995 - JP 2018138019-A/164921: Polycomb-Associated Non-Coding RNAs.
MA592994 - JP 2018138019-A/164920: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K8S9, ENST00000343090.1, ENST00000343090.10, ENST00000343090.2, ENST00000343090.3, ENST00000343090.4, ENST00000343090.5, ENST00000343090.6, ENST00000343090.7, ENST00000343090.8, ENST00000343090.9, G0ZJH6, HDNB1 , KIAA0684 , NM_001105562, O75169, O95155, O95338, Q5SZ12, Q5SZ16, Q96QD4, Q9BYI7, UBE4B , UBE4B_HUMAN, uc317wnw.1, uc317wnw.2, UFD2
UCSC ID: ENST00000343090.11_4
RefSeq Accession: NM_001105562.3
Protein: O95155 (aka UBE4B_HUMAN or UB4B_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.