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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0005524ATP bindingIEAUniProtKB-KW:KW-0067GO_REF:0000037559
GO:0016881acid-amino acid ligase activityIEAIPR000608GO_REF:000000245
GO:0005515protein bindingIPIptr3PMID:23416107861
GO:0004842ubiquitin-protein transferase activityISSUniProtKB:P15731GO_REF:000002476
has substrate cdc13IDAPMID:12724208
has substrate san1IMPPMID:21324894
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0008054cyclin catabolic processIGIcdc13PMID:1272440812
GO:0000070mitotic sister chromatid segregation130
requiredIMPPMID:8972853
GO:0071630nucleus-associated proteasomal ubiquitin-dependent protein catabolic process4
regulates cia1IMPPMID:21324894
GO:0000209protein polyubiquitinationISSUniProtKB:P15731GO_REF:00000244
GO:0016485protein processing37
has input sre2IMPPMID:23729666
GO:0016567protein ubiquitinationIMPPMID:21324894109
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005737cytoplasmIDAPMID:213248944201
GO:0005829cytosolIDAPMID:168233722316
GO:0005634nucleusIDAPMID:213248942740
IDAPMID:16823372
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationnot recorded (unrecorded)PMID:127244081315
Microscopyubc4ΔNullPMID:20473289
Microscopyubc4ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0001357normal vegetative cell population growthCell growth assayubc4ts (P61S)PECO:0000137, PECO:0000005PMID:21324894466
FYPO:0000082sensitive to heatCell growth assayubc4ts (P61S)PECO:0000137PMID:21324894138

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopyubc4ΔNullPECO:0000005, PECO:0000137PMID:23697806624
FYPO:0000912abolished protein ubiquitination7
affecting ubc4Enzyme assay dataL10D (L10D)Not specifiedPMID:23416107
FYPO:0001422decreased protein processing12
affecting sre2Western blot assayubc4-P61S (P61S)Not specifiedPMID:23729666
FYPO:0002768decreased protein ubiquitination5
affecting ubc4Enzyme assay dataL30A (L30A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataL119A (L119A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataN7D (N7D)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataD28R (D28R)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataL30A,F31A (L30A, F31A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataD28A (D28A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataN79Y,L119A (N79Y, L119A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataN79A (N79A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataP121A (P121A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataP118A (P118A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataD116A (D116A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataA124F (A124F)Not specifiedPMID:23416107
FYPO:0001991inviable after spore germination, without cell divisionMicroscopyubc4ΔNullPECO:0000005, PECO:0000137PMID:23697806468
FYPO:0002635normal protein ubiquitination5
affecting ubc4Enzyme assay dataS108A (S108A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataS108D (S108D)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataH125A (H125A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataR90A (R90A)Not specifiedPMID:23416107
affecting ubc4Enzyme assay dataK128A (K128A)Not specifiedPMID:23416107
FYPO:0001492viable elongated vegetative cell182
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
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 18
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)DuringConditionScaleEvidenceReference
42054.17during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
33683.72during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
305467during GO:0072690PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
315701during GO:0000084PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
306990during GO:0000080PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
339257during GO:0000087PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
283788during GO:0000085PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
8during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
52during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
conserved in fungi4569
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3393
conserved in eukaryotes only2487
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
ubc11ubiquitin conjugating enzyme E2-C, Ubc11 Phenotypic EnhancementPMID:23442800
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 Phenotypic SuppressionPMID:21324894
Synthetic Growth Defect
mis6inner centromere protein, CENP-I ortholog Mis6 Synthetic RescuePMID:24497846
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
cul3cullin 3 Affinity Capture-MSPMID:14527422
epe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
ptr3ubiquitin activating enzyme E1 Reconstituted ComplexPMID:23416107
bdf2BET family double bromodomain protein Bdf2 Affinity Capture-MSPMID:24013502
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)
IntEnz6.3.2.19Integrated relational Enzyme database
Rhea6.3.2.19Annotated reactions database
EntrezGene2540083ubiquitin conjugating enzyme Ubc4
WikiGene2540083ubiquitin conjugating enzyme Ubc4
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 ArchiveCAA17917ENA Protein Mapping
European Nucleotide ArchiveCAA17917.1ENA Protein Mapping
UniParcUPI0000137961UniProt Archive

Literature for ubc4

Search: Europe PMC or PubMed

Release Version: PomBase:22_44 - 08 Jul 2014