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 tag5
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
meiotic cell cycle430
Annotation ExtensionEvidenceWith/FromReference
protein ubiquitination117
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
viable vegetative cell populationubi4ΔNull3792

Cell Phenotype

Term NameAlleleExpressionCount
abnormal meiotic spindleubi4-H45 (M1V)Not specified10
abolished meiosisubi4-H45 (M1V)Not specified17
abolished sporulationubi4-H45 (M1V)Not specified54
ubi4ΔNull
decreased sporulationubi4-1 (monoubiquitin)Not specified70
normal horsetail nucleus morphologyubi4-H45 (M1V)Not specified2
normal premeiotic DNA replicationubi4-H45 (M1V)Not specified16
viable vegetative cell with normal cell morphologyubi4ΔNull3092
Target Of
OntologyRelationshipGeneProductReference
GO substrate of ptr3 ubiquitin activating enzyme E1 PMID:23416107
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-like 158 226 14
PF00240 Pfam IPR000626 Ubiquitin-like 234 302 14
PF00240 Pfam IPR000626 Ubiquitin-like 82 150 14
PF00240 Pfam IPR000626 Ubiquitin-like 310 378 14
PF00240 Pfam IPR000626 Ubiquitin-like 6 74 14
SM00213 SMART IPR000626 Ubiquitin-like 153 224 13
SM00213 SMART IPR000626 Ubiquitin-like 305 376 13
SM00213 SMART IPR000626 Ubiquitin-like 229 300 13
SM00213 SMART IPR000626 Ubiquitin-like 1 72 13
SM00213 SMART IPR000626 Ubiquitin-like 77 148 13
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 305 380 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 77 152 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 229 304 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 153 228 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 1 76 18
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
PTHR10666 HMMPANTHER 1 380 6
PTHR10666:SF112 HMMPANTHER 1 380 1
3.10.20.90 Gene3D 305 379 28
3.10.20.90 Gene3D 155 229 28
3.10.20.90 Gene3D 79 154 28
3.10.20.90 Gene3D 1 78 28
3.10.20.90 Gene3D 230 304 28
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 228 304 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 304 380 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 76 152 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 1 76 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 151 228 29
PR00348 PRINTS IPR019956 Ubiquitin 32 52 6
PR00348 PRINTS IPR019956 Ubiquitin 53 74 6
PR00348 PRINTS IPR019956 Ubiquitin 11 31 6

View domain organization at Pfam

Manually Curated Family or Sub-families

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
Isoelectric point 7.85
Molecular weight 42.97 kDa
Number of residues 382
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1672
present during cellular response to thiabendazoleS361
present during cellular response to thiabendazoleS209
present during cellular response to thiabendazoleS57
present during cellular response to thiabendazoleS133
present during cellular response to thiabendazoleS285
Annotation ExtensionEvidenceResidueReference
present during cellular response to thiabendazole IDA S57 PMID:18257517
present during cellular response to thiabendazole IDA S133 PMID:18257517
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 S361 PMID:18257517
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
RNA levelincreased during GO:0051321Northern assay evidencePMID:10623474
present during GO:0072690Northern assay evidencePMID:10623474

Quantitative Gene Expression

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
9.7during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
6.7during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4604
conserved in eukaryotes4516
conserved in metazoa3430
conserved in vertebrates3405
conserved in eukaryotes only2502
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
affinity capturesaat1amino acid transmembrane transporter Aat1 Affinity Capture-WesternPMID:22194353
affinity capturesaat1amino acid transmembrane transporter Aat1 Affinity Capture-WesternPMID:24454826
affinity captured byany1arrestin-related endocytic adaptor Any1 Affinity Capture-WesternPMID:24876389
affinity capturescat1cationic amino acid transmembrane transporter Cat1 Affinity Capture-WesternPMID:24876389
affinity captured bycat1cationic amino acid transmembrane transporter Cat1 Affinity Capture-WesternPMID:24876389
affinity captured bycbf11CBF1/Su(H)/LAG-1 family transcription factor Cbf11 Affinity Capture-MSPMID:22540037
affinity captured bycdc18MCM loader Affinity Capture-WesternPMID:9203581
affinity capturescnp1centromere-specific histone H3 CENP-A Affinity Capture-WesternPMID:25298518
forms complex withcul1cullin 1 Reconstituted ComplexPMID:11337588
forms complex withdsc2Golgi Dsc E3 ligase complex subunit Dsc2 Reconstituted ComplexPMID:23760507
affinity captured bydsc2Golgi Dsc E3 ligase complex subunit Dsc2 Affinity Capture-WesternPMID:23760507
forms complex withimp2contractile ring protein Imp2 Reconstituted ComplexPMID:19139265
affinity capturesmei2RNA-binding protein involved in meiosis Mei2 Affinity Capture-WesternPMID:24741065
affinity capturesmei2RNA-binding protein involved in meiosis Mei2 Affinity Capture-WesternPMID:11702950
affinity capturesmik1mitotic inhibitor kinase Mik1 Affinity Capture-WesternPMID:10637286
affinity capturespap1transcription factor Pap1/Caf3 Affinity Capture-WesternPMID:23209828
affinity captured bypcn1PCNA Affinity Capture-WesternPMID:20452294
affinity capturespcn1PCNA Affinity Capture-WesternPMID:16641370
ptr3ubiquitin activating enzyme E1 Co-crystal or NMR structurePMID:23416107
forms complex withpus1tRNA pseudouridine synthase Lsp1 Reconstituted ComplexPMID:23038266
forms complex withrhp23Rad23 homolog Rhp23 Reconstituted ComplexPMID:23038266
forms complex withrhp23Rad23 homolog Rhp23 Reconstituted ComplexPMID:17211518
forms complex withrhp23Rad23 homolog Rhp23 Reconstituted ComplexPMID:25306921
forms complex withrpn15proteasome regulatory particle, lid subcomplex subunit Rpn15/Dss1 Reconstituted ComplexPMID:25306921
affinity captured byrum1CDK inhibitor Rum1 Affinity Capture-WesternPMID:9203581
affinity captured bysid4SIN component scaffold protein Sid4 Affinity Capture-WesternPMID:24055157
affinity capturesslp1mitotic spindle checkpoint component/ APC activator Slp1 Affinity Capture-WesternPMID:23442800
affinity capturesspc7NMS complex subunit, Spc105/KNL-1 family member, blinkin, Spc7 Affinity Capture-WesternPMID:24497846
modified byubc11ubiquitin conjugating enzyme E2-C, Ubc11/UbcP4 Biochemical ActivityPMID:23442800
affinity captureszip1transcription factor Zip1 Affinity Capture-WesternPMID:15660136
Genetic Interactions

Source: BioGRID

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)
Cyclebase SPBC337.08c Cell Cycle Data
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
SPD / RIKEN40/40D01Orfeome Localization Data
UniProtKB/SwissProtP0CG72Polyubiquitin
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:25_50 - 10 Mar 2015