ubc4 (SPBC119.02)


Gene Standard Nameubc4 Characterisation Statuspublished
Systematic IDSPBC119.02 Feature Typeprotein coding
Synonyms Name Description
Productubiquitin conjugating enzyme Ubc4 Product Size147aa, 16.48 kDa
Genomic Location Chromosome II, 715227-716311 (1085nt); CDS:715333-716226 (894nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding558
Annotation ExtensionEvidenceWith/FromReference
protein binding831
Annotation ExtensionEvidenceWith/FromReference
small conjugating protein ligase activity24
Annotation ExtensionEvidenceWith/FromReference
ubiquitin conjugating enzyme activity10
Annotation ExtensionEvidenceWith/FromReference
ubiquitin-protein transferase activity73
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
mitotic sister chromatid segregation192
Annotation ExtensionEvidenceWith/FromReference
protein polyubiquitination5
Annotation ExtensionEvidenceWith/FromReference
protein processing112
Annotation ExtensionEvidenceWith/FromReference
protein ubiquitination115
Annotation ExtensionEvidenceWith/FromReference
protein ubiquitination involved in ubiquitin-dependent protein catabolic process14
Annotation ExtensionEvidenceWith/FromReference
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process6
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytoplasm4205
Annotation ExtensionEvidenceWith/FromReference
cytosol2315
Annotation ExtensionEvidenceWith/FromReference
nuclear SCF ubiquitin ligase complex5
Annotation ExtensionEvidenceWith/FromReference
nucleus2740
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000082decreased cell population growth at high temperatureCell growth assayubc4ts (P61S)PECO:0000137PMID:21324894148
FYPO:0002061inviable vegetative cell populationMicroscopyubc4ΔNullPECO:0000005, PECO:0000137PMID:236978061338
Microscopyubc4ΔNullPMID:20473289
Microscopynot recorded (unrecorded)PMID:12724408
FYPO:0001357normal vegetative cell population growthCell growth assayubc4ts (P61S)PECO:0000137, PECO:0000005PMID:21324894641

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopyubc4ΔNullPECO:0000005, PECO:0000137PMID:23697806686
FYPO:0000912abolished protein ubiquitination7
affecting ubc4Enzyme assay dataL10D (L10D)Not specifiedPMID:23416107
FYPO:0003585decreased anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process3
affecting cdc13Western blot assayubc4-P61S (P61S)Not specifiedPECO:0000004PMID:23442800
affecting cut2Western blot assayubc4-P61S (P61S)Not specifiedPECO:0000004PMID:23442800
FYPO:0001422decreased protein processing12
affecting sre2Western blot assayubc4-P61S (P61S)Not specifiedPMID:23729666
FYPO:0002768decreased protein ubiquitination6
affecting ubc4Enzyme assay dataN79A (N79A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataN79Y,L119A (N79Y, L119A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataL30A,F31A (L30A, F31A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataD28A (D28A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataN7D (N7D)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataD28R (D28R)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataL30A (L30A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataL119A (L119A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataD116A (D116A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataP118A (P118A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataA124F (A124F)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataP121A (P121A)Not specifiedPMID:23416107
FYPO:0001991inviable after spore germination, without cell divisionMicroscopyubc4ΔNullPECO:0000005, PECO:0000137PMID:23697806474
FYPO:0003594normal anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process2
affecting slp1Western blot assayubc4-P61S (P61S)Not specifiedPECO:0000004PMID:23442800
FYPO:0002635normal protein ubiquitination5
affecting ubc4Enzyme assay dataH125A (H125A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataR90A (R90A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataK128A (K128A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataS108A (S108A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataS108D (S108D)Not specifiedPMID:23416107
FYPO:0001492viable elongated vegetative cell221
penetrance FYPO_EXT:0000003Microscopyubc4ΔNullPECO:0000006, PECO:0000137PMID:23697806
Target Of
OntologyRelationshipGeneProductReference
FYPO affected by mutation in ptr3 ubiquitin activating enzyme E1 PMID:23416107
FYPO affected by mutation in ubc4 ubiquitin conjugating enzyme Ubc4 PMID:23416107
GO substrate of ptr3 ubiquitin activating enzyme E1 PMID:25165823
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1715227715452
2715532715609
3715981716311

UTRs

Region Coordinates Reference
five_prime_UTR715227..715332PMID:21511999
three_prime_UTR716227..716311PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF00179 Pfam IPR000608 Ubiquitin-conjugating enzyme, E2 5 141 14
SM00212 SMART 4 147 14
PS00183 Prosite Patterns IPR023313 Ubiquitin-conjugating enzyme, active site 74 89 10
PS50127 Prosite Profiles IPR000608 Ubiquitin-conjugating enzyme, E2 4 136 14
PTHR24068 HMMPANTHER 1 146 1
3.10.110.10 Gene3D IPR016135 Ubiquitin-conjugating enzyme/RWD-like 1 146 19
SSF54495 SuperFamily IPR016135 Ubiquitin-conjugating enzyme/RWD-like 1 146 19

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.08 Da
Charge 1.00
Isoelectric point 6.93
Molecular weight 16.48 kDa
Number of residues 147
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
306990during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
315701during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
283788during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
339257during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
305467during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
42054.17during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
33683.72during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
52during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
8during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
conserved in eukaryotes only2497
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
cul3cullin 3 Affinity Capture-MSPMID:14527422
ptr3ubiquitin activating enzyme E1 Reconstituted ComplexPMID:23416107
fbh1DNA helicase I Reconstituted ComplexPMID:25165823
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
apm1AP-1 adaptor complex mu subunit Apm1 Dosage RescuePMID:24454826
ubc11ubiquitin conjugating enzyme E2-C, Ubc11 Phenotypic EnhancementPMID:23442800
ecm33cell wall protein Ecm33 Dosage RescuePMID:24454826
cis4cation diffusion family zinc membrane transporter Cis4 Dosage RescuePMID:24454826
mal2kinetochore protein, CENP-O ortholog Mal2 Synthetic RescuePMID:24497846
cdc42Rho family GTPase Cdc42 Phenotypic SuppressionPMID:10628977
spc7kinetochore protein blinkin, Spc7 Synthetic RescuePMID:24497846
cia1histone chaperone Cia1 Synthetic Growth DefectPMID:21324894
Phenotypic Suppression
mis6inner centromere protein, CENP-I ortholog Mis6 Synthetic RescuePMID:24497846
External References
Database Identifier Description
NBRP SPBC119.02 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC119.02 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC119.02 BioGRID Interaction Datasets
Expression Viewer SPBC119.02 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC119.02 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC119.02 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC119.02 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC119.02 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC119.02 Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC119.02 Cell Cycle Data
GEO SPBC119.02 GEO profiles
PInt SPBC119.02 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC119.02 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC119.02 Fission yeast phenotypic data & analysis
IntEnz6.3.2.19Integrated relational Enzyme database
Rhea6.3.2.19Annotated reactions database
SPD / RIKEN32/32A10Orfeome Localization Data
UniProtKB/SwissProtP46595Ubiquitin-conjugating enzyme E2 4
ModBaseP46595Database of comparative protein structure models
STRINGP46595Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595283ubiquitin conjugating enzyme Ubc4
RefSeq mRNANM_001021190972h- ubiquitin conjugating enzyme Ubc4 (ubc4), mRNA
European Nucleotide ArchiveL37384ENA EMBL mapping
ePDB4II2The European PDB
PDB4II2PDB
PDBsum4II2PDBsum
European Nucleotide ArchiveCAA17917.1ENA Protein Mapping
UniParcUPI0000137961UniProt Archive

Literature for ubc4

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014