ubp3 (SPBP8B7.21)


Gene Standard Nameubp3 Characterisation Statuspublished
Systematic IDSPBP8B7.21 Feature Typeprotein coding
Synonyms Name Description
Productubiquitin C-terminal hydrolase Ubp3 Product Size512aa, 58.08 kDa
Genomic Location Chromosome II, 3676896-3679661 (2766nt); CDS:3677713-3679289 (1577nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
protein binding856
Annotation ExtensionEvidenceWith/FromReference
ubiquitin-specific protease activity26
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
protein deubiquitination23
Annotation ExtensionEvidenceWith/FromReference
proteolysis298
Annotation ExtensionEvidenceWith/FromReference
regulation of ER to Golgi vesicle-mediated transport2
Annotation ExtensionEvidenceWith/FromReference
ubiquitin-dependent protein catabolic process187
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytoplasm4207
Annotation ExtensionEvidenceWith/FromReference
cytosol2314
Annotation ExtensionEvidenceWith/FromReference
nucleus2695
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
normal growth on cisplatinubp3ΔNull39
normal growth on glucose carbon sourceubp3ΔNull203
sensitive to hydroxyureaubp3ΔNull534
viable vegetative cell populationubp3ΔNull3795

Cell Phenotype

Term NameAlleleExpressionCount
viable vegetative cell with normal cell morphologyubp3ΔNull3093
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons3676896..3677793, 3677832..3679661
mRNA3676896..3679661
5' UTR3676896..3677712PMID:21511999
CDS3677713..3677793, 3677832..3679289
3' UTR3679290..3679661PMID: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
PF00443 Pfam IPR001394 Peptidase C19, ubiquitin carboxyl-terminal hydrolase 133 508 15
PS00972 Prosite Patterns IPR018200 Ubiquitin specific protease, conserved site 134 149 12
PS00973 Prosite Patterns IPR018200 Ubiquitin specific protease, conserved site 436 454 14
PS50235 Prosite Profiles IPR028889 Ubiquitin specific protease domain 133 511 16
PTHR24006 HMMPANTHER 90 512 13
PTHR24006:SF367 HMMPANTHER 90 512 2
SSF54001 SuperFamily 298 510 30
SSF54001 SuperFamily 122 269 30

View domain organization at Pfam

Protein Properties

Ave. residue weight 113.44 Da
Charge 5.00
Isoelectric point 7.03
Molecular weight 58.08 kDa
Number of residues 512
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1672
present during mitotic M phaseS89
S89, S281, S282
level fluctuates during mitotic cell cycleS89
Annotation ExtensionEvidenceResidueReference
IDA S89 PMID:21182284
present during mitotic M phase experimental evidence S89 PMID:21712547
level fluctuates during mitotic cell cycle experimental evidence S89 PMID:24763107
IDA S281 PMID:21182284
IDA S282 PMID:21182284
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1905during GO:0000080PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
1603during GO:0000085PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
2127during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
2828.4during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
4848.49during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
4.9during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
0.82during 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 capturesmts419S proteasome regulatory subunit Mts4 Affinity Capture-WesternPMID:24497846
affinity capturesnxt3ubiquitin protease cofactor Glp1 (predicted) Affinity Capture-WesternPMID:22328580
affinity captured bynxt3ubiquitin protease cofactor Glp1 (predicted) Affinity Capture-MSPMID:22328580
affinity capturesnxt3ubiquitin protease cofactor Glp1 (predicted) Affinity Capture-MSPMID:20838651
affinity captured bysog2leucine-rich repeat protein Lrp1 Affinity Capture-MSPMID:23462181
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
positive genetic interaction withagn1glucan endo-1,3-alpha-glucosidase Agn1 Positive GeneticPMID:22681890
rescuesago1argonaute Phenotypic SuppressionPMID:21892171
negative genetic interaction withair1zinc knuckle TRAMP complex subunit Air1 Negative GeneticPMID:18818364
positive genetic interaction withamo1nuclear rim protein Amo1 Positive GeneticPMID:18818364
positive genetic interaction withapq12nuclear membrane organization protein Apq12 (predicted) Positive GeneticPMID:22681890
negative genetic interaction witharp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:18818364
negative genetic interaction witharp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:22681890
positive genetic interaction withask1DASH complex subunit Ask1 Positive GeneticPMID:18818364
positive genetic interaction withask1DASH complex subunit Ask1 Positive GeneticPMID:22681890
rescuesasp1inositol hexakisphosphate kinase/inositol pyrophosphate synthase (predicted) Phenotypic SuppressionPMID:19547744
positive genetic interaction withatg7E1 Atg8 and Atg12 E1 activating enzyme Atg7 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withath1ataxin-2 homolog Positive GeneticPMID:22681890
positive genetic interaction withatp11mitochondrial F1-ATPase chaperone Atp11 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withbtf3nascent polypeptide-associated complex beta subunit Positive GeneticPMID:22681890
positive genetic interaction withbun107WD repeat protein, human WDR48 family Bun107 Positive GeneticPMID:22681890
negative genetic interaction withcay1cactin, spliceosome complex subunit (predicted) Negative GeneticPMID:18818364
positive genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:18818364
negative genetic interaction withcgi121EKC/KEOPS complex subunit Cgi121 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withcho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Positive GeneticPMID:18818364
positive genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:18818364
positive genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:22681890
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:18818364
positive genetic interaction withdad2DASH complex subunit Dad2 Positive GeneticPMID:18818364
positive genetic interaction withdad2DASH complex subunit Dad2 Positive GeneticPMID:22681890
negative genetic interaction withddb1damaged DNA binding protein Ddb1 Negative GeneticPMID:22681890
synthetic growth defect withdlc2dynein light chain Dlc2 (predicted) Synthetic Growth DefectPMID:18931302
negative genetic interaction withdsk1SR protein-specific kinase Dsk1 Negative GeneticPMID:22681890
positive genetic interaction withelp1elongator subunit Elp1 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withelp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withelp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withelp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withelp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withelp4elongator complex subunit Elp4 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withelp6elongator complex subunit Elp6 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withfft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:18818364
positive genetic interaction withfft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:22681890
positive genetic interaction withfta6Mis6-Sim4 complex Fta6 Positive GeneticPMID:22681890
positive genetic interaction withgcn5SAGA complex histone acetyltransferase catalytic subunit Gcn5 Positive GeneticPMID:22681890
positive genetic interaction withgmh5alpha-1,2-galactosyltransferase (predicted) Positive GeneticPMID:18818364
negative genetic interaction withhip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
positive genetic interaction withhrp1ATP-dependent DNA helicase Hrp1 Positive GeneticPMID:18818364
positive genetic interaction withhrq1RecQ type DNA helicase Hrq1 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withhrq1RecQ type DNA helicase Hrq1 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withhrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Positive GeneticPMID:18818364
negative genetic interaction withiwr1RNA polymerase II nuclear import protein Iwr1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withknk1AAA family ATPase kink, Knk1 Positive GeneticPMID:22681890
negative genetic interaction withleo1RNA polymerase II associated Paf1 complex (predicted) Negative GeneticPMID:18818364
positive genetic interaction withmaf1repressor of RNA polymerase III Maf1 Positive GeneticPMID:22681890
positive genetic interaction withmcl1DNA polymerase alpha accessory factor Mcl1 Positive GeneticPMID:22681890
negative genetic interaction withmde6Muskelin homolog (predicted) Negative GeneticPMID:22681890
positive genetic interaction withmed20mediator complex subunit Med20 Positive GeneticPMID:18818364
positive genetic interaction withmei4meiotic forkhead transcription factor Mei4 Positive GeneticPMID:18818364
negative genetic interaction withmga2IPT/TIG ankyrin repeat containing transcription regulator of fatty acid biosynthesis (predicted) Negative GeneticPMID:18818364
negative genetic interaction withmkh1MEK kinase (MEKK) Mkh1 Negative GeneticPMID:22681890
negative genetic interaction withmlh1MutL family protein Mlh1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withmmb1mitochondrial microtubule binder Mmb1 Negative GeneticPMID:22681890
positive genetic interaction withmms19Dos2 silencing complex subunit Mms19 Positive GeneticPMID:18818364
negative genetic interaction withmms19Dos2 silencing complex subunit Mms19 Negative GeneticPMID:22681890
positive genetic interaction withmrpl1mitochondrial ribosomal protein subunit L1 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withmsh1mitochondrial MutS protein Msh1 (predicted) Positive GeneticPMID:18818364
negative genetic interaction withmug33Tea1-interacting protein involved in exocytosis Negative GeneticPMID:22681890
negative genetic interaction withmug80cyclin Clg1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withnht1Ino80 complex HMG box subunit Nht1 Negative GeneticPMID:22681890
rescuesnrm1MBF complex corepressor Nrm1 Phenotypic SuppressionPMID:19547744
positive genetic interaction withpck1protein kinase C (PKC)-like Pck1 Positive GeneticPMID:22681890
rescuespck1protein kinase C (PKC)-like Pck1 Phenotypic SuppressionPMID:19547744
negative genetic interaction withpef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:22681890
negative genetic interaction withpek1MAP kinase kinase Pek1 Negative GeneticPMID:18818364
negative genetic interaction withpfa3palmitoyltransferase Pfa3 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withpnk1DNA kinase/phosphatase Pnk1 Positive GeneticPMID:18818364
enhances phenotype ofpof2F-box protein Pof2 Phenotypic EnhancementPMID:19547744
positive genetic interaction withppk14serine/threonine protein kinase Ppk14 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withppk30Ark1/Prk1 family protein kinase Ppk30 Positive GeneticPMID:18818364
negative genetic interaction withptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
positive genetic interaction withptc2protein phosphatase 2C Ptc2 Positive GeneticPMID:18818364
negative genetic interaction withptn1phosphatidylinositol-3,4,5-trisphosphate3-phosphatase Ptn1 Negative GeneticPMID:18818364
negative genetic interaction withpun1SUR7 family protein Pun1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withpyp1tyrosine phosphatase Pyp1 Negative GeneticPMID:22681890
phenotype enhanced bypyp1tyrosine phosphatase Pyp1 Phenotypic EnhancementPMID:19547744
rescued bypyp2tyrosine phosphatase Pyp2 Phenotypic SuppressionPMID:19547744
positive genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:18818364
positive genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:22681890
positive genetic interaction withraf2Rik1-associated factor Raf2 Positive GeneticPMID:18818364
negative genetic interaction withrap1telomere binding protein Rap1 Negative GeneticPMID:18818364
negative genetic interaction withrap1telomere binding protein Rap1 Negative GeneticPMID:22681890
positive genetic interaction withreb1RNA polymerase I transcription termination factor/ RNA polymerase II transcription factor Reb1 Positive GeneticPMID:18818364
positive genetic interaction withreb1RNA polymerase I transcription termination factor/ RNA polymerase II transcription factor Reb1 Positive GeneticPMID:22681890
negative genetic interaction withrec14Ski complex subunit Rec14 Negative GeneticPMID:18818364
positive genetic interaction withres2MBF transcription factor complex subunit Res2 Positive GeneticPMID:18818364
positive genetic interaction withrhn1RNA polymerase II transcription termination factor homolog Positive GeneticPMID:22681890
positive genetic interaction withsck2serine/threonine protein kinase Sck2 Positive GeneticPMID:24463365
positive genetic interaction withscs7sphingosine hydroxylase Scs7 Positive GeneticPMID:18818364
negative genetic interaction withsdh4TIM22 inner membrane protein import complex anchor subunit Tim18 Negative GeneticPMID:22681890
positive genetic interaction withser2phosphoserine phosphatase Ser2 (predicted) Positive GeneticPMID:18818364
negative genetic interaction withset1histone lysine methyltransferase Set1 Negative GeneticPMID:18818364
negative genetic interaction withsft1SNARE Sft1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withsgf29SAGA complex subunit Sgf29 Positive GeneticPMID:18818364
negative genetic interaction withSPAC1071.09cDNAJ domain protein, DNAJC9 family (predicted) Negative GeneticPMID:22681890
positive genetic interaction withSPAC1093.03inositol polyphosphate phosphatase (predicted) Positive GeneticPMID:18818364
negative genetic interaction withSPAC10F6.13caspartate aminotransferase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC1142.02cTPR repeat protein, SGT2 family (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC11G7.01serine-rich Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withSPAC15A10.07Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withSPAC15E1.02cDUF1761 family protein Negative GeneticPMID:22681890
negative genetic interaction withSPAC1805.10Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withSPAC1F12.04cconserved fungal protein Negative GeneticPMID:22681890
positive genetic interaction withSPAC212.04cS. pombe specific DUF999 family protein 1 Positive GeneticPMID:22681890
positive genetic interaction withSPAC227.17cconserved protein Positive GeneticPMID:22681890
positive genetic interaction withSPAC3H1.06ctransmembrane transporter (predicted) Positive GeneticPMID:22681890
negative genetic interaction withSPAC977.05cconserved fungal family Negative GeneticPMID:22681890
negative genetic interaction withSPBC3F6.01cserine/threonine protein phosphatase (predicted) Negative GeneticPMID:22681890
positive genetic interaction withspc34DASH complex subunit Spc34 Positive GeneticPMID:18818364
synthetically rescuesspc7NMS complex subunit, Spc105/KNL-1 family member, blinkin, Spc7 Synthetic RescuePMID:24497846
overexpression causes growth defect tospc7NMS complex subunit, Spc105/KNL-1 family member, blinkin, Spc7 Dosage Growth DefectPMID:24497846
rescuesspc7NMS complex subunit, Spc105/KNL-1 family member, blinkin, Spc7 Phenotypic SuppressionPMID:24497846
negative genetic interaction withSPCC584.11cSvf1 family protein Svf1 Negative GeneticPMID:22681890
positive genetic interaction withsrb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
positive genetic interaction withssb3DNA replication factor A subunit Ssb3 Positive GeneticPMID:22681890
positive genetic interaction withsts5RNB-like protein Positive GeneticPMID:22681890
negative genetic interaction withsut1alpha-glucoside transmembrane transporter Sut1 Negative GeneticPMID:22681890
negative genetic interaction withswd1Set1C complex subunit Swd1 Negative GeneticPMID:22681890
negative genetic interaction withswd2Set1C complex subunit Swd2.1 Negative GeneticPMID:18818364
negative genetic interaction withswd3WD repeat protein Swd3 Negative GeneticPMID:18818364
negative genetic interaction withtfs1transcription elongation factor TFIIS Negative GeneticPMID:22681890
negative genetic interaction withtor1phosphatidylinositol kinase Tor1 Negative GeneticPMID:22681890
positive genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:18818364
positive genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:22681890
negative genetic interaction withvps38phophatidylinositol 3-kinase complex subunit Vps38 Negative GeneticPMID:22681890
positive genetic interaction withxap5xap-5-like protein Positive GeneticPMID:24957674
positive genetic interaction withzip1transcription factor Zip1 Positive GeneticPMID:22681890
External References
Database Identifier Description
NBRP SPBP8B7.21 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBP8B7.21 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBP8B7.21 BioGRID Interaction Datasets
Expression Viewer SPBP8B7.21 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBP8B7.21 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBP8B7.21 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBP8B7.21 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBP8B7.21 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBP8B7.21 Transcriptome Viewer (Bähler Lab)
GEO SPBP8B7.21 GEO profiles
PInt SPBP8B7.21 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBP8B7.21 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBP8B7.21 Fission yeast phenotypic data & analysis
Cyclebase SPBP8B7.21.1 Cell Cycle Data
SPD / RIKEN25/25D05Orfeome Localization Data
UniProtKB/SwissProtO94269Probable ubiquitin carboxyl-terminal hydrolase 3
ModBaseO94269Database of comparative protein structure models
STRINGO94269Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596528ubiquitin C-terminal hydrolase Ubp3
RefSeq mRNANM_001022449972h- ubiquitin C-terminal hydrolase Ubp3 (ubp3), mRNA
European Nucleotide ArchiveCAA21806.1ENA Protein Mapping
UniParcUPI00001379DDUniProt Archive

Literature for ubp3

Search: Europe PMC or PubMed

Release Version: PomBase:26_51 - 07 Apr 2015