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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0031386protein tagNASGO_REF:00000015
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0051321meiotic cell cycle223
requiredIMPPMID:10623474
GO:0016567protein ubiquitinationNASGO_REF:0000001108
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005634nucleusIEAUniProtKB-KW:KW-0539GO_REF:00000372740
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002060viable vegetative cell populationMicroscopyubi4ΔNullPMID:204732893730
Microscopyubi4ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001Microscopyubi4ΔNullPECO:0000005, PECO:0000137PMID:23697806
Target Of
OntologyRelationshipGeneProductReference
GO substrate of ptr3 ubiquitin activating enzyme E1 PMID:23416107
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
110466421044271

UTRs

Region Coordinates Reference
five_prime_UTR1046642..1045567PMID: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
PF00240 Pfam IPR000626 Ubiquitin-like 310 378 14
PF00240 Pfam IPR000626 Ubiquitin-like 6 74 14
PF00240 Pfam IPR000626 Ubiquitin-like 82 150 14
PF00240 Pfam IPR000626 Ubiquitin-like 234 302 14
PF00240 Pfam IPR000626 Ubiquitin-like 158 226 14
SM00213 SMART IPR000626 Ubiquitin-like 77 148 13
SM00213 SMART IPR000626 Ubiquitin-like 1 72 13
SM00213 SMART IPR000626 Ubiquitin-like 229 300 13
SM00213 SMART IPR000626 Ubiquitin-like 153 224 13
SM00213 SMART IPR000626 Ubiquitin-like 305 376 13
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 331 356 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 255 280 7
PS00299 Prosite Patterns IPR019954 Ubiquitin conserved site 179 204 7
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 153 228 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 229 304 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 1 76 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 305 380 18
PS50053 Prosite Profiles IPR000626 Ubiquitin-like 77 152 18
PTHR10666:SF112 HMMPANTHER 1 380 1
PTHR10666 HMMPANTHER 1 380 6
3.10.20.90 Gene3D 155 229 28
3.10.20.90 Gene3D 1 78 28
3.10.20.90 Gene3D 305 379 28
3.10.20.90 Gene3D 79 154 28
3.10.20.90 Gene3D 230 304 28
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 151 228 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 228 304 29
SSF54236 SuperFamily IPR029071 Ubiquitin-related domain 304 380 29
PR00348 PRINTS IPR019956 Ubiquitin 53 74 6
PR00348 PRINTS IPR019956 Ubiquitin 32 52 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 IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineIDAS361PMID:182575171669
present during cellular response to thiabendazole
present during cellular response to thiabendazoleIDAS285PMID:18257517
present during cellular response to thiabendazoleIDAS209PMID:18257517
present during cellular response to thiabendazoleIDAS133PMID:18257517
present during cellular response to thiabendazoleIDAS57PMID:18257517
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
NDduring GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
9.7during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
6.7during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
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
cis4cation diffusion family zinc membrane transporter Cis4 Dosage RescuePMID:24454826
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
zip1transcription factor Zip1 Affinity Capture-WesternPMID:15660136
pcn1PCNA Affinity Capture-WesternPMID:20452294
Affinity Capture-WesternPMID:16641370
mei2RNA-binding protein involved in meiosis Mei2 Affinity Capture-WesternPMID:11702950
cbf11CBF1/Su(H)/LAG-1 family transcription factor Cbf11 Affinity Capture-MSPMID:22540037
rhp23Rad23 homolog Rhp23 Reconstituted ComplexPMID:23038266
Reconstituted ComplexPMID:17211518
rum1CDK inhibitor Rum1 Affinity Capture-WesternPMID:9203581
pus1tRNA pseudouridine synthase Lsp1 Reconstituted ComplexPMID:23038266
mik1mitotic inhibitor kinase Mik1 Affinity Capture-WesternPMID:10637286
bdf2BET family double bromodomain protein Bdf2 Affinity Capture-MSPMID:24013502
slp1sleepy homolog Slp1 Affinity Capture-WesternPMID:23442800
imp2contractile ring protein Imp2 Reconstituted ComplexPMID:19139265
cdc18MCM loader Affinity Capture-WesternPMID:9203581
dsc2Golgi Dsc E3 ligase complex subunit Dsc2 Affinity Capture-WesternPMID:23760507
Reconstituted Complex
spc7kinetochore protein blinkin, Spc7 Affinity Capture-WesternPMID:24497846
aat1amino acid transporter Aat1 Affinity Capture-WesternPMID:22194353
Affinity Capture-WesternPMID:24454826
ubc11ubiquitin conjugating enzyme E2-C, Ubc11 Biochemical ActivityPMID:23442800
sid4SIN component scaffold protein Sid4 Affinity Capture-WesternPMID:24055157
pap1transcription factor Pap1/Caf3 Affinity Capture-WesternPMID:23209828
ptr3ubiquitin activating enzyme E1 Co-crystal or NMR structurePMID:23416107
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
WikiGene2541030ubiquitin
EntrezGene2541030ubiquitin
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 ArchiveAAC64787ENA Protein Mapping
European Nucleotide ArchiveCAA21278ENA Protein Mapping
European Nucleotide ArchiveCAA21278.1ENA Protein Mapping
UniParcUPI00001620BEUniProt Archive

Literature for ubi4

Search: Europe PMC or PubMed

Release Version: PomBase:22_45 - 08 Aug 2014