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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0005515protein bindingIPInxt3PMID:20838651861
GO:0004843ubiquitin-specific protease activityIDAPMID:2083865126
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0016579protein deubiquitinationIDAPMID:2083865124
GO:0006508proteolysisIDAPMID:20838651271
GO:0060628regulation of ER to Golgi vesicle-mediated transportISOSGD:S000000953GO_REF:00000242
GO:0006511ubiquitin-dependent protein catabolic processIEAIPR001394GO_REF:0000002173
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005737cytoplasmIDAPMID:208386514201
GO:0005829cytosolIDAPMID:168233722316
GO:0005634nucleusIDAPMID:168233722740
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001023normal growth on cisplatinCell growth assayubp3ΔNullPECO:0000137, PECO:0000103, PECO:0000005PMID:2124741636
FYPO:0001164normal growth on glucose carbon sourceCell growth assayubp3ΔNullPECO:0000137, PECO:0000005, PECO:0000102PMID:24497846156
FYPO:0000088sensitive to hydroxyurea511
expressivity FYPO_EXT:0000003Cell Growth Assayubp3ΔNullPECO:0000137, PECO:0000102PMID:23697806
FYPO:0002060viable vegetative cell populationMicroscopyubp3ΔNullPMID:204732893730
Microscopyubp3ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001Microscopyubp3ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
136768963677793
236778323679661

UTRs

Region Coordinates Reference
five_prime_UTR3676896..3677712PMID:21511999
three_prime_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 Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site 134 149 12
PS00973 Prosite Patterns IPR018200 Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site 436 454 14
PS50235 Prosite Profiles IPR028889 Ubiquitin carboxyl-terminal hydrolase-like domain 133 512 16
PTHR24006:SF367 HMMPANTHER 90 512 2
PTHR24006 HMMPANTHER 90 512 13
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 IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineS89PMID:217125471669
present during mitotic M phase
level fluctuates during mitotic cell cycleS89PMID:24763107
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

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

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
4.9during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
0.82during 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
med20mediator complex subunit Med20 Positive GeneticPMID:18818364
pnk1DNA kinase/phosphatase Pnk1 Positive GeneticPMID:18818364
alf1ATP-dependent microtubule severing protein (predicted) Positive GeneticPMID:22681890
mga2IPT/TIG ankyrin repeat containing transcription regulator of fatty acid biosynthesis (predicted) Negative GeneticPMID:18818364
pef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:22681890
fta6Sim4 and Mal2 associated (4 and 2 associated) protein 6 Positive GeneticPMID:22681890
swd1Set1C complex subunit Swd1 Negative GeneticPMID:22681890
elp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
mms19Dos2 silencing complex subunit Mms19 Positive GeneticPMID:18818364
Negative GeneticPMID:22681890
SPAC1F12.04cconserved fungal protein Negative GeneticPMID:22681890
gcn5SAGA complex histone acetyltransferase catalytic subunit Gcn5 Positive GeneticPMID:22681890
dad2DASH complex subunit Dad2 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
rap1telomere binding protein Rap1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
mcl1DNA polymerase alpha accessory factor Mcl1 Positive GeneticPMID:22681890
sft1SNARE Sft1 (predicted) Negative GeneticPMID:22681890
amo1nuclear rim protein Amo1 Positive GeneticPMID:18818364
ccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:18818364
mei4meiotic forkhead transcription factor Mei4 Positive GeneticPMID:18818364
sts5RNB-like protein Positive GeneticPMID:22681890
hip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
spc34DASH complex subunit Spc34 Positive GeneticPMID:18818364
zip1transcription factor Zip1 Positive GeneticPMID:22681890
asp1inositol hexakisphosphate kinase/inositol pyrophosphate synthase (predicted) Phenotypic SuppressionPMID:19547744
SPAC15E1.02cDUF1761 family protein Negative GeneticPMID:22681890
SPAC227.17cconserved protein Positive GeneticPMID:22681890
leo1RNA polymerase II associated Paf1 complex (predicted) Negative GeneticPMID:18818364
mlh1MutL family protein Mlh1 (predicted) Negative GeneticPMID:22681890
fft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
pun1SUR7 family protein Pun1 (predicted) Negative GeneticPMID:22681890
agn1glucan endo-1,3-alpha-glucosidase Agn1 Positive GeneticPMID:22681890
SPAC1610.02cmitochondrial ribosomal protein subunit L1 (predicted) Positive GeneticPMID:22681890
ago1argonaute Phenotypic SuppressionPMID:21892171
elp4elongator complex subunit Elp4 (predicted) Positive GeneticPMID:18818364
SPBC3F6.01cserine/threonine protein phosphatase (predicted) Negative GeneticPMID:22681890
ath1ataxin-2 homolog Positive GeneticPMID:22681890
rec14Ski complex subunit Rec14 Negative GeneticPMID:18818364
raf2Rik1-associated factor Raf2 Positive GeneticPMID:18818364
btf3nascent polypeptide-associated complex beta subunit Positive GeneticPMID:22681890
elp1elongator subunit Elp1 (predicted) Positive GeneticPMID:18818364
gmh5alpha-1,2-galactosyltransferase (predicted) Positive GeneticPMID:18818364
elp6elongator complex subunit Elp6 (predicted) Positive GeneticPMID:18818364
mug80cyclin Clg1 (predicted) Negative GeneticPMID:22681890
vps38phophatidylinositol 3-kinase complex subunit Vps38 Negative GeneticPMID:22681890
cph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:18818364
SPCC584.11cSvf1 family protein Svf1 Negative GeneticPMID:22681890
sck2serine/threonine protein kinase Sck2 Positive GeneticPMID:24463365
mmb1mitochondria microtubule binder Mmb1 Negative GeneticPMID:22681890
atp11F1-ATPase chaperone Atp11 (predicted) Positive GeneticPMID:22681890
srb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
sgf29SAGA complex subunit Sgf29 Positive GeneticPMID:18818364
hrp1ATP-dependent DNA helicase Hrp1 Positive GeneticPMID:18818364
SPAC1805.10sequence orphan Negative GeneticPMID:22681890
pyp2tyrosine phosphatase Pyp2 Phenotypic SuppressionPMID:19547744
SPAC212.04cS. pombe specific DUF999 family protein 1 Positive GeneticPMID:22681890
ser2phosphoserine phosphatase Ser2 (predicted) Positive GeneticPMID:18818364
air1zinc knuckle TRAMP complex subunit Air1 Negative GeneticPMID:18818364
msh1mitochondrial MutS protein Msh1 (predicted) Positive GeneticPMID:18818364
ddb1damaged DNA binding protein Ddb1 Negative GeneticPMID:22681890
elp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
sdh4TIM22 inner membrane protein import complex anchor subunit Tim18 Negative GeneticPMID:22681890
set1histone lysine methyltransferase Set1 Negative GeneticPMID:18818364
iwr1RNA polymerase II nuclear import protein Iwr1 (predicted) Negative GeneticPMID:22681890
mug33Tea1-interacting protein involved in exocytosis Negative GeneticPMID:22681890
clr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
pek1MAP kinase kinase Pek1 Negative GeneticPMID:18818364
cho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Positive GeneticPMID:18818364
apq12nuclear membrane organization protein Apq12 (predicted) Positive GeneticPMID:22681890
pck1protein kinase C (PKC)-like Pck1 Positive GeneticPMID:22681890
Phenotypic SuppressionPMID:19547744
ppk30Ark1/Prk1 family protein kinase Ppk30 Positive GeneticPMID:18818364
nrm1MBF complex corepressor Nrm1 Phenotypic SuppressionPMID:19547744
mde6Muskelin homolog (predicted) Negative GeneticPMID:22681890
arp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
hrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Positive GeneticPMID:18818364
ptc2protein phosphatase 2C Ptc2 Positive GeneticPMID:18818364
sut1alpha-glucoside transporter Sut1 Negative GeneticPMID:22681890
rhn1RNA polymerase II transcription termination factor homolog Positive GeneticPMID:22681890
reb1RNA polymerase I transcription termination factor Reb1 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
SPAC1071.09cDNAJ domain protein, DNAJC9 family (predicted) Negative GeneticPMID:22681890
SPAC1093.03inositol polyphosphate phosphatase (predicted) Positive GeneticPMID:18818364
pyp1tyrosine phosphatase Pyp1 Negative GeneticPMID:22681890
Phenotypic EnhancementPMID:19547744
SPAC15A10.07sequence orphan Negative GeneticPMID:22681890
SPAC11G7.01sequence orphan Negative GeneticPMID:22681890
swd2Set1C complex subunit Swd2.1 Negative GeneticPMID:18818364
scs7sphingosine hydroxylase Scs7 Positive GeneticPMID:18818364
SPAC3H1.06cmembrane transporter (predicted) Positive GeneticPMID:22681890
swd3WD repeat protein Swd3 Negative GeneticPMID:18818364
maf1repressor of RNA polymerase III Maf1 Positive GeneticPMID:22681890
tor1phosphatidylinositol kinase Tor1 Negative GeneticPMID:22681890
cgi121EKC/KEOPS complex subunit Cgi121 (predicted) Negative GeneticPMID:22681890
SPAC10F6.08cHMG box protein Negative GeneticPMID:22681890
ssb3DNA replication factor A subunit Ssb3 Positive GeneticPMID:22681890
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
mkh1MEK kinase (MEKK) Mkh1 Negative GeneticPMID:22681890
ask1DASH complex subunit Ask1 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
hrq1RecQ type DNA helicase Hrq1 (predicted) Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
atg7E1 ubiquitin-like conjugating enzyme Atg7 Positive GeneticPMID:22681890
dlc2dynein light chain Dlc2 (predicted) Synthetic Growth DefectPMID:18931302
ptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
dsk1SR protein-specific kinase Dsk1 Negative GeneticPMID:22681890
ppk14serine/threonine protein kinase Ppk14 (predicted) Positive GeneticPMID:22681890
SPAC977.05cconserved fungal family Negative GeneticPMID:22681890
ptn1phosphatidylinositol-3,4,5-trisphosphate3-phosphatase Ptn1 Negative GeneticPMID:18818364
cay1cactin, spliceosome complex subunit (predicted) Negative GeneticPMID:18818364
res2MBF transcription factor complex subunit Res2 Positive GeneticPMID:18818364
SPAC1142.02cTPR repeat protein, SGT2 family (predicted) Negative GeneticPMID:22681890
pfa3palmitoyltransferase Pfa3 (predicted) Negative GeneticPMID:22681890
raf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
bun107WD repeat protein, human WDR48 family Bun107 Positive GeneticPMID:22681890
tfs1transcription elongation factor TFIIS Negative GeneticPMID:22681890
spc7kinetochore protein blinkin, Spc7 Synthetic RescuePMID:24497846
Phenotypic Suppression
Dosage Growth Defect
SPAC10F6.13caspartate aminotransferase (predicted) Negative GeneticPMID:22681890
pof2F-box protein Pof2 Phenotypic EnhancementPMID:19547744
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
hhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
hhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
nxt3ubiquitin protease cofactor Glp1 (predicted) Affinity Capture-MSPMID:22328580
Affinity Capture-Western
Affinity Capture-MSPMID:20838651
mts419S proteasome regulatory subunit Mts4 Affinity Capture-WesternPMID:24497846
sog2leucine-rich repeat protein Lrp1 Affinity Capture-MSPMID:23462181
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)
Cyclebase SPBP8B7.21 Cell Cycle Data
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
SPD / RIKEN25/25D05Orfeome Localization Data
WikiGene2541378ubiquitin C-terminal hydrolase Ubp3
EntrezGene2541378ubiquitin C-terminal hydrolase Ubp3
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 ArchiveCAA21806ENA Protein Mapping
European Nucleotide ArchiveCAA21806.1ENA Protein Mapping
UniParcUPI00001379DDUniProt Archive

Literature for ubp3

Search: Europe PMC or PubMed

Release Version: PomBase:22_45 - 08 Aug 2014