ubi4 (SPBC337.08c)


Gene Standard Nameubi4 Characterisation Statuspublished
Systematic IDSPBC337.08c Feature Typeprotein coding
Synonyms Name Description
Productubiquitin Product Size382aa, 42.97 kDa
Genomic Location Chromosome II, 1046642-1044271 (2372nt); CDS:1045566-1044418 (1149nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
protein binding887
Annotation ExtensionEvidenceWith/FromReference
protein tag5
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
meiotic cell cycle236
Annotation ExtensionEvidenceWith/FromReference
protein ubiquitination99
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
decreased sporulation frequencyubi4-1 (monoubiquitin)103
viable vegetative cell populationubi4Δ3850

Cell Phenotype

Term NameGenotypesCount
abnormal meiotic spindleubi4-H45 (M1V)14
abolished meiosisubi4-H45 (M1V)20
abolished protein binding147
affecting rpn15 and ubi4I44A (I44A)
affecting rhp23 and ubi4I44A (I44A)
abolished sporulationubi4Δ56
ubi4-H45 (M1V)
normal horsetail nucleus morphologyubi4-H45 (M1V)4
normal premeiotic DNA replicationubi4-H45 (M1V)25
viable vegetative cell with normal cell morphologyubi4Δ3102
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in rpn15 proteasome regulatory particle, lid subcomplex subunit Rpn15/Dss1
FYPO affected by mutation in ubi4 ubiquitin
GO substrate of ptr3 ubiquitin activating enzyme E1
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1046642..1044271
mRNA1046642..1044271
5' UTR1046642..1045567PMID:21511999
CDS1045566..1044418
3' UTR1044417..1044271AU011508
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
PF00240 Pfam IPR000626 Ubiquitin domain 155 226 14
PF00240 Pfam IPR000626 Ubiquitin domain 231 302 14
PF00240 Pfam IPR000626 Ubiquitin domain 307 378 14
PF00240 Pfam IPR000626 Ubiquitin domain 3 74 14
PF00240 Pfam IPR000626 Ubiquitin domain 79 150 14
SM00213 SMART IPR000626 Ubiquitin domain 153 224 13
SM00213 SMART IPR000626 Ubiquitin domain 1 72 13
SM00213 SMART IPR000626 Ubiquitin domain 77 148 13
SM00213 SMART IPR000626 Ubiquitin domain 305 376 13
SM00213 SMART IPR000626 Ubiquitin domain 229 300 13
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 255 280 7
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 27 52 7
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 103 128 7
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 331 356 7
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 179 204 7
PS50053 Prosite Profiles IPR000626 Ubiquitin domain 153 228 18
PS50053 Prosite Profiles IPR000626 Ubiquitin domain 305 380 18
PS50053 Prosite Profiles IPR000626 Ubiquitin domain 77 152 18
PS50053 Prosite Profiles IPR000626 Ubiquitin domain 1 76 18
PS50053 Prosite Profiles IPR000626 Ubiquitin domain 229 304 18
PTHR10666:SF150 HMMPANTHER 1 381 1
PTHR10666 HMMPANTHER 1 381 6
3.10.20.90 Gene3D Rho guanine nucleotide exchange factor Cdc24/Scd1 305 379 28
3.10.20.90 Gene3D Rho guanine nucleotide exchange factor Cdc24/Scd1 1 78 28
3.10.20.90 Gene3D Rho guanine nucleotide exchange factor Cdc24/Scd1 155 229 28
3.10.20.90 Gene3D Rho guanine nucleotide exchange factor Cdc24/Scd1 79 154 28
3.10.20.90 Gene3D Rho guanine nucleotide exchange factor Cdc24/Scd1 230 304 28
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 1 76 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 228 304 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 76 152 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 151 228 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 304 380 29
PR00348 PRINTS IPR019956 Ubiquitin 32 52 6
PR00348 PRINTS IPR019956 Ubiquitin 11 31 6
PR00348 PRINTS IPR019956 Ubiquitin 53 74 6

View domain organization at Pfam

Term IDTerm NameReferenceCount
PBO:0001447ubiquitin family proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001447

Protein Properties

Ave. residue weight 112.49 Da
Charge 2.50
Codon Adaptation Index 0.72
Isoelectric point 7.85
Molecular weight 42.97 kDa
Number of residues 382
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 2289
present during cellular response to thiabendazoleS209
present during cellular response to thiabendazoleS285
present during cellular response to thiabendazoleS57
present during cellular response to thiabendazoleS361
present during cellular response to thiabendazoleS133
Annotation ExtensionEvidenceResidueReference
present during cellular response to thiabendazole IDA S209 PMID:18257517
present during cellular response to thiabendazole IDA S285 PMID:18257517
present during cellular response to thiabendazole IDA S57 PMID:18257517
present during cellular response to thiabendazole IDA S361 PMID:18257517
present during cellular response to thiabendazole IDA S133 PMID:18257517
ubiquitinylated lysineK6, K11, K27, K29, K33, K48, K63, K87 512
Annotation ExtensionEvidenceResidueReference
mass spectrometry evidence K87 PMID:26412298
mass spectrometry evidence K6 PMID:26412298
mass spectrometry evidence K27 PMID:26412298
IDA PMID:26412298
mass spectrometry evidence K29 PMID:26412298
mass spectrometry evidence K63 PMID:26412298
mass spectrometry evidence K48 PMID:26412298
mass spectrometry evidence K33 PMID:26412298
mass spectrometry evidence K11 PMID:26412298
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
RNA levelpresent during GO:0072690Northern assay evidencePMID:10623474
increased during GO:0051321Northern assay evidencePMID:10623474

Quantitative Gene Expression

View graphical display of gene expression data for ubi4 (SPBC337.08c)

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
9.7during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
6.7during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3093
conserved in fungi4607
conserved in eukaryotes4517
conserved in metazoa3427
conserved in vertebrates3402
conserved in eukaryotes only2502
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC337.08c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity capturescnp1centromere-specific histone H3 CENP-A Affinity Capture-WesternPMID:25298518
affinity capturesaat1amino acid transmembrane transporter Aat1 Affinity Capture-WesternPMID:22194353
affinity capturesmei2RNA-binding protein involved in meiosis Mei2 Affinity Capture-WesternPMID:24741065
affinity capturesslp1substrate-specific mitotic metaphase/anaphase APC coactivator Slp1 Affinity Capture-WesternPMID:23442800
affinity capturesmik1mitotic inhibitor kinase Mik1 Affinity Capture-WesternPMID:10637286
affinity capturespcn1PCNA Affinity Capture-WesternPMID:16641370
affinity capturespap1transcription factor Pap1/Caf3 Affinity Capture-WesternPMID:23209828
affinity captureszip1transcription factor Zip1 Affinity Capture-WesternPMID:15660136
forms complex withpus1tRNA pseudouridine synthase Lsp1 Reconstituted ComplexPMID:23038266
forms complex withmud1UBA domain protein Mud1 Reconstituted ComplexPMID:22095407
forms complex withcul1cullin 1 Reconstituted ComplexPMID:11337588
forms complex withrpn15proteasome regulatory particle, lid subcomplex subunit Rpn15/Dss1 Reconstituted ComplexPMID:25306921
forms complex withrhp23Rad23 homolog Rhp23 Reconstituted ComplexPMID:23038266
forms complex withdsc2Golgi Dsc E3 ligase complex subunit Dsc2 Reconstituted ComplexPMID:23760507
forms complex withimp2contractile ring protein Imp2 Reconstituted ComplexPMID:19139265
affinity captured bypcn1PCNA Affinity Capture-WesternPMID:20452294
affinity captured bycdc18MCM loader Affinity Capture-WesternPMID:9203581
affinity captured byrum1CDK inhibitor Rum1 Affinity Capture-WesternPMID:9203581
affinity captured bycbf11CBF1/Su(H)/LAG-1 family transcription factor Cbf11 Affinity Capture-MSPMID:22540037
modified byubc11ubiquitin conjugating enzyme E2, Ubc11/UbcP4 Biochemical ActivityPMID:23442800
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBC337.08c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
overexpression rescuescis4cation diffusion family zinc transmembrane transporter Cis4 Dosage RescuePMID:24454826
External References
Database Identifier Description
NBRP SPBC337.08c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC337.08c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC337.08c BioGRID Interaction Datasets
Expression Viewer SPBC337.08c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC337.08c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC337.08c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC337.08c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC337.08c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC337.08c Transcriptome Viewer (Bähler Lab)
GEO SPBC337.08c GEO profiles
PInt SPBC337.08c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC337.08c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC337.08c Fission yeast phenotypic data & analysis
Cyclebase SPBC337.08c.1 Cell Cycle Data
SPD / RIKEN40/40D01Orfeome Localization Data
UniProtKB/SwissProtP0CG72Polyubiquitin Ubiquitin
ModBaseP0CG72Database of comparative protein structure models
STRINGP0CG72Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595409ubiquitin
RefSeq mRNANM_001021316972h- ubiquitin (ubi4), mRNA
European Nucleotide ArchiveCAA21278.1ENA Protein Mapping
UniParcUPI00001620BEUniProt Archive

Literature for ubi4

Search: Europe PMC or PubMed

Release Version: PomBase:30_61 - 12 Sep 2016