ubp4 (SPBC18H10.08c)


Gene Standard Nameubp4 Characterisation Statuspublished
Systematic IDSPBC18H10.08c Feature Typeprotein coding
Synonyms Name Description
Productubiquitin C-terminal hydrolase Ubp4 Product Size593aa, 67.75 kDa
Genomic Location Chromosome II, 1786542-1783861 (2682nt); CDS:1786248-1784219 (2030nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005515protein bindingIPIsfp47PMID:20838651865
GO:0004843ubiquitin-specific protease activityIDAPMID:2083865126
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0016579protein deubiquitinationIDAPMID:2083865124
GO:0006508proteolysisIDAPMID:20838651273
GO:0006511ubiquitin-dependent protein catabolic processIEAIPR001394GO_REF:0000002175
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0032153cell division siteIDAPMID:20838651298
GO:0005737cytoplasmIDAPMID:168233724204
GO:0005768endosomeIDAPMID:2083865178
GO:0030133transport vesicleIDAPMID:2083865138
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001023normal growth on cisplatinCell growth assayubp4ΔNullPECO:0000137, PECO:0000103, PECO:0000005PMID:2124741636
FYPO:0000088sensitive to hydroxyureaCell growth assayubp4ΔNullPECO:0000137, PECO:0000005PMID:23173672513
FYPO:0002060viable vegetative cell populationMicroscopyubp4ΔNullPECO:0000005, PECO:0000137PMID:236978063751
Microscopyubp4ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001Microscopyubp4ΔNullPECO:0000005, PECO:0000137PMID:23697806
Target Of
OntologyRelationshipGeneProductReference
GO localized by sfp47 Ubp4 interactor Sfp47 PMID:20838651
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
117865421786475
217864341786141
317860801785937
417857481783861
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 227 570 15
PS00973 Prosite Patterns IPR018200 Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site 514 531 14
PS00972 Prosite Patterns IPR018200 Peptidase C19, ubiquitin carboxyl-terminal hydrolase, conserved site 228 243 12
PS50235 Prosite Profiles IPR028889 Ubiquitin carboxyl-terminal hydrolase-like domain 227 574 16
PTHR24006 HMMPANTHER 1 593 14
PTHR24006:SF44 HMMPANTHER 1 593 1
SSF54001 SuperFamily 226 572 30

View domain organization at Pfam

Protein Properties

Ave. residue weight 114.25 Da
Charge 14.00
Isoelectric point 8.16
Molecular weight 67.75 kDa
Number of residues 593
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineIDAS343PMID:211822841670
MOD:00696phosphorylated residueNASPMID:195477441922
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
6597during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
617.72during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.23during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Warning
DescriptionQualifierReferenceCount
gene structure updated432
Species Distribution
DescriptionQualifierReferenceCount
conserved in fungi4599
conserved in eukaryotes4514
conserved in metazoa3428
conserved in vertebrates3402
conserved in eukaryotes only2498
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
med20mediator complex subunit Med20 Negative GeneticPMID:18818364
exg1glucan 1,6-beta-glucosidase Exg1 Negative GeneticPMID:22681890
sle1eisosome assembly protein Seg1 Negative GeneticPMID:22681890
hip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
mug117conserved fungal protein Mug117 Negative GeneticPMID:22681890
msh6MutS protein homolog Negative GeneticPMID:22681890
SPAC227.11csensor for misfolded ER glycoproteins Yos9 (predicted) Negative GeneticPMID:22681890
swd1Set1C complex subunit Swd1 Negative GeneticPMID:18818364
mpc2mitochondrial pyruvate transmembrane transporter Mpc2 (predicted) Negative GeneticPMID:22681890
met11methylenetetrahydrofolate reductase Met11 Negative GeneticPMID:22681890
rad55RecA family ATPase Rad55/Rhp55 Negative GeneticPMID:22681890
lys4homocitrate synthase Negative GeneticPMID:22681890
zhf1zinc ion transporter Zhf1 Negative GeneticPMID:22681890
dsc3Golgi Dsc E3 ligase complex subunit Dsc3 Negative GeneticPMID:21504829
pmc5mediator complex subunit Pmc5 Negative GeneticPMID:18818364
sib1ferrichrome synthetase Sib1 Negative GeneticPMID:22681890
cao1copper amine oxidase Cao1 Negative GeneticPMID:22681890
rga8Rho-type GTPase activating protein Rga8 Negative GeneticPMID:22681890
ccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:18818364
oga1Stm1 homolog Oga1 Negative GeneticPMID:22681890
pcf3CAF assembly factor (CAF-1) complex subunit C, Pcf3 Negative GeneticPMID:22681890
emc1ER membrane protein complex subunit Emc1 (predicted) Negative GeneticPMID:22681890
aru1arginase Aru1 Negative GeneticPMID:22681890
pcf2CAF assembly factor (CAF-1) complex subunit B, Pcf2 Negative GeneticPMID:22681890
SPBC4B4.04translation initiation factor eIF2A (predicted) Negative GeneticPMID:18818364
ryh1GTPase Ryh1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
sum2G2/M transition checkpoint protein Sum2 Negative GeneticPMID:18818364
gpa2heterotrimeric G protein alpha-2 subunit Gpa2 Negative GeneticPMID:22681890
lys12homoisocitrate dehydrogenase Lys12 Negative GeneticPMID:22681890
SPCC594.06cvacuolar SNARE Vam7 (predicted) Positive GeneticPMID:22681890
ckb2CK2 family regulatory subunit Ckb2 (predicted) Negative GeneticPMID:22681890
mug191alpha-1,6- mannanase (predicted) Positive GeneticPMID:22681890
SPBC1271.14glutamate N-acetyltransferase (predicted) Negative GeneticPMID:22681890
cph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:18818364
arg12argininosuccinate synthase Arg12 Negative GeneticPMID:22681890
rkr1RQC complex ubiquitin-protein ligase E3 Rkr1 (predicted) Positive GeneticPMID:22681890
sgf29SAGA complex subunit Sgf29 Negative GeneticPMID:18818364
SPAC10F6.15UPF0300 family protein 1 Negative GeneticPMID:22681890
mug96Schizosaccharomyces pombe specific protein Negative GeneticPMID:22681890
lys3saccharopine dehydrogenase Lys3 Negative GeneticPMID:22681890
hrp3ATP-dependent DNA helicase Hrp3 Positive GeneticPMID:22681890
SPAC644.13cRab GTPase binding (predicted) Negative GeneticPMID:22681890
tip1CLIP170 family protein Tip1 Positive GeneticPMID:22681890
SPAC17H9.13cglutamate 5-kinase (predicted) Negative GeneticPMID:22681890
lys2homoaconitate hydratase Lys2 Negative GeneticPMID:22681890
rqc1ribosome quality control complex (RQC) complex subunit Rqc1 (predicted) Negative GeneticPMID:22681890
ubp2ubiquitin C-terminal hydrolase Ubp2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
SPAC328.04AAA family ATPase, unknown biological role Negative GeneticPMID:22681890
vps24ESCRT III complex subunit Vps24 Phenotypic EnhancementPMID:19547744
mal1maltase alpha-glucosidase Mal1 Positive GeneticPMID:22681890
SPBC887.08Schizosaccharomyces specific protein Negative GeneticPMID:22681890
set1histone lysine methyltransferase Set1 Negative GeneticPMID:18818364
snz1pyridoxine biosynthesis protein Negative GeneticPMID:22681890
SPAC29A4.17cmitochondrial FUN14 family protein Negative GeneticPMID:22681890
pek1MAP kinase kinase Pek1 Negative GeneticPMID:22681890
SPAC12B10.15cribonuclease H2 complex subunit (predicted) Negative GeneticPMID:22681890
arg11N-acetyl-gamma-glutamyl-phosphate reductase/acetylglutamate kinase Negative GeneticPMID:22681890
mug114sSchizosaccharomyces pombe specific protein Mug114 Negative GeneticPMID:22681890
vps1dynamin family protein Vps1 Negative GeneticPMID:22681890
SPAC1D4.01human C9orf78 ortholog Negative GeneticPMID:22681890
SPAC750.04cS. pombe specific 5Tm protein family Negative GeneticPMID:22681890
ssr3SWI/SNF and RSC complex subunit Ssr3 Negative GeneticPMID:22681890
pit1serine/threonine protein kinase, meiotic Pit1 Positive GeneticPMID:22681890
rsc4RSC complex subunit Rsc4 Positive GeneticPMID:22681890
arp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:18818364
SPAC4H3.06human C19orf60 homolog Negative GeneticPMID:22681890
spf1Set1C PHD Finger protein Spf1 Negative GeneticPMID:18818364
myp2myosin II heavy chain Myo3 Negative GeneticPMID:22681890
SPAPB1A10.05Schizosaccharomyces specific protein Negative GeneticPMID:22681890
hhp2serine/threonine protein kinase Hhp2 Negative GeneticPMID:22681890
SPAC13G7.11mitochondrial respiratory complex assembly protein (predicted) Positive GeneticPMID:22681890
swd3WD repeat protein Swd3 Negative GeneticPMID:22681890
skb5Shk1 kinase binding protein 5 Positive GeneticPMID:22681890
sil1nucleotide exchange factor for the ER lumenal Hsp70 chaperone, Sil1 (predicted) Positive GeneticPMID:22681890
SPAC105.02cankyrin repeat protein, implicated in meiosis Negative GeneticPMID:22681890
cyp3cyclophilin family peptidyl-prolyl cis- trans isomerase Cyp3 Positive GeneticPMID:22681890
SPBC409.17cDUF1769 family protein Negative GeneticPMID:22681890
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:18818364
SPAC212.08cS. pombe specific GPI anchored protein family 1 Positive GeneticPMID:22681890
SPAC13G6.08Cdc20/Fizzy subfamily WD repeat protein Positive GeneticPMID:22681890
SPAC1071.05S-adenosylmethionine-dependent methyltransferase (predicted) Positive GeneticPMID:22681890
alm1medial ring protein Alm1 Negative GeneticPMID:22681890
sac12inositol polyphosphate phosphatase (predicted) Positive GeneticPMID:22681890
SPAC1039.06alanine racemase (predicted) Negative GeneticPMID:22681890
SPAC1A6.01chuman thyroid receptor interacting protein homolog, transcription coactivator (predicted) Negative GeneticPMID:22681890
SPBC1709.16caromatic ring-opening dioxygenase (predicted) Negative GeneticPMID:22681890
arg6acetylglutamate synthase Arg6 (predicted) Negative GeneticPMID:22681890
spa2GTPase activating protein Spa2 (predicted) Negative GeneticPMID:22681890
SPAC11D3.03cconserved protein Negative GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
sfp47Ubp4 interactor Sfp47 Affinity Capture-MSPMID:20838651
Affinity Capture-Western
crp79poly(A) binding protein Crp79 Affinity Capture-RNAPMID:20531409
External References
Database Identifier Description
NBRP SPBC18H10.08c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC18H10.08c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC18H10.08c BioGRID Interaction Datasets
Expression Viewer SPBC18H10.08c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC18H10.08c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC18H10.08c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC18H10.08c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC18H10.08c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC18H10.08c Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC18H10.08c Cell Cycle Data
GEO SPBC18H10.08c GEO profiles
PInt SPBC18H10.08c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC18H10.08c Peptides identified in tandem mass spectrometry proteomics experiments
SPD / RIKEN44/44C04Orfeome Localization Data
UniProtKB/SwissProtO60139Probable ubiquitin carboxyl-terminal hydrolase 4
ModBaseO60139Database of comparative protein structure models
STRINGO60139Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595732ubiquitin C-terminal hydrolase Ubp4
RefSeq mRNANM_001021630972h- ubiquitin C-terminal hydrolase Ubp4 (ubp4), mRNA
European Nucleotide ArchiveCAA18405.2ENA Protein Mapping
UniParcUPI000228F499UniProt Archive

Literature for ubp4

Search: Europe PMC or PubMed

Release Version: PomBase:23_46 - 30 Aug 2014