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 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
ubiquitin-dependent protein catabolic process187
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cell division site305
Annotation ExtensionEvidenceWith/FromReference
cytoplasm4207
Annotation ExtensionEvidenceWith/FromReference
endosome80
Annotation ExtensionEvidenceWith/FromReference
transport vesicle39
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
normal growth on cisplatinubp4ΔNull39
sensitive to hydroxyureaubp4ΔNull534
viable vegetative cell populationubp4ΔNull3795

Cell Phenotype

Term NameAlleleExpressionCount
viable vegetative cell with normal cell morphologyubp4ΔNull3093
Target Of
OntologyRelationshipGeneProductReference
GO localized by sfp47 Ubp4 interactor Sfp47 PMID:20838651
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1786542..1786475, 1786434..1786141, 1786080..1785937, 1785748..1783861
mRNA1786542..1783861
5' UTR1786542..1786475, 1786434..1786249PMID:21511999
CDS1786248..1786141, 1786080..1785937, 1785748..1784219
3' UTR1784218..1783861PMID:20118936
3' UTR1784218..1783861PMID:18641648
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 Ubiquitin specific protease, conserved site 514 531 14
PS00972 Prosite Patterns IPR018200 Ubiquitin specific protease, conserved site 228 243 12
PS50235 Prosite Profiles IPR028889 Ubiquitin specific protease domain 227 573 16
PTHR24006 HMMPANTHER 17 585 13
PTHR24006:SF332 HMMPANTHER 17 585 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 NameResidueCount
O-phospho-L-serineS343 1672
Annotation ExtensionEvidenceResidueReference
IDA S343 PMID:21182284
phosphorylated residue 1926
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
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

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 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 captured bycrp79poly(A) binding protein Crp79 Affinity Capture-RNAPMID:20531409
affinity capturessfp47Ubp4 interactor Sfp47 Affinity Capture-MSPMID:20838651
affinity capturessfp47Ubp4 interactor Sfp47 Affinity Capture-WesternPMID:20838651
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withalm1medial ring protein Alm1 Negative GeneticPMID:22681890
negative genetic interaction witharg11N-acetyl-gamma-glutamyl-phosphate reductase/acetylglutamate kinase Negative GeneticPMID:22681890
negative genetic interaction witharg12argininosuccinate synthase Arg12 Negative GeneticPMID:22681890
negative genetic interaction witharg6acetylglutamate synthase Arg6 (predicted) Negative GeneticPMID:22681890
negative genetic interaction witharp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:18818364
negative genetic interaction witharu1arginase Aru1 Negative GeneticPMID:22681890
negative genetic interaction withcao1copper amine oxidase Cao1 Negative GeneticPMID:22681890
positive genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:18818364
negative genetic interaction withckb2CK2 family regulatory subunit Ckb2 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:18818364
positive genetic interaction withcyp3cyclophilin family peptidyl-prolyl cis- trans isomerase Cyp3 Positive GeneticPMID:22681890
negative genetic interaction withdsc3Golgi Dsc E3 ligase complex subunit Dsc3 Negative GeneticPMID:21504829
negative genetic interaction witheif21translation initiation factor eIF2A (predicted) Negative GeneticPMID:18818364
negative genetic interaction withemc1ER membrane protein complex subunit Emc1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withexg1glucan 1,6-beta-glucosidase Exg1 Negative GeneticPMID:22681890
negative genetic interaction withgpa2heterotrimeric G protein alpha-2 subunit Gpa2 Negative GeneticPMID:22681890
negative genetic interaction withhhp2serine/threonine protein kinase Hhp2 Negative GeneticPMID:22681890
negative genetic interaction withhip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
positive genetic interaction withhrp3ATP-dependent DNA helicase Hrp3 Positive GeneticPMID:22681890
negative genetic interaction withlys12homoisocitrate dehydrogenase Lys12 Negative GeneticPMID:22681890
negative genetic interaction withlys2homoaconitate hydratase Lys2 Negative GeneticPMID:22681890
negative genetic interaction withlys3saccharopine dehydrogenase Lys3 Negative GeneticPMID:22681890
negative genetic interaction withlys4homocitrate synthase Negative GeneticPMID:22681890
positive genetic interaction withmal1maltase alpha-glucosidase Mal1 Positive GeneticPMID:22681890
positive genetic interaction withmba1mitochondrial respiratory complex assembly protein Mba1 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withmed20mediator complex subunit Med20 Negative GeneticPMID:18818364
negative genetic interaction withmed6mediator complex subunit Med6 Negative GeneticPMID:18818364
negative genetic interaction withmet11methylenetetrahydrofolate reductase Met11 Negative GeneticPMID:22681890
negative genetic interaction withmpc2mitochondrial pyruvate transmembrane transporter Mpc2 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withmsh6MutS protein homolog Negative GeneticPMID:22681890
negative genetic interaction withmug114Schizosaccharomyces pombe specific protein Mug114 Negative GeneticPMID:22681890
negative genetic interaction withmug117conserved fungal protein Mug117 Negative GeneticPMID:22681890
positive genetic interaction withmug191alpha-1,6- mannanase (predicted) Positive GeneticPMID:22681890
negative genetic interaction withmug96Schizosaccharomyces pombe specific protein Negative GeneticPMID:22681890
negative genetic interaction withmyp2myosin II heavy chain Myo3 Negative GeneticPMID:22681890
negative genetic interaction withoga1Stm1 homolog Oga1 Negative GeneticPMID:22681890
negative genetic interaction withpcf2CAF assembly factor (CAF-1) complex subunit B, Pcf2 Negative GeneticPMID:22681890
negative genetic interaction withpcf3CAF assembly factor (CAF-1) complex subunit C, Pcf3 Negative GeneticPMID:22681890
negative genetic interaction withpek1MAP kinase kinase Pek1 Negative GeneticPMID:22681890
positive genetic interaction withpit1serine/threonine protein kinase, meiotic Pit1 Positive GeneticPMID:22681890
negative genetic interaction withrad55RecA family ATPase Rad55/Rhp55 Negative GeneticPMID:22681890
negative genetic interaction withrga8Rho-type GTPase activating protein Rga8 Negative GeneticPMID:22681890
positive genetic interaction withrkr1RQC complex ubiquitin-protein ligase E3 Rkr1 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withrqc1ribosome quality control complex (RQC) complex subunit Rqc1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withrsc4RSC complex subunit Rsc4 Positive GeneticPMID:22681890
negative genetic interaction withryh1GTPase Ryh1 Negative GeneticPMID:18818364
negative genetic interaction withryh1GTPase Ryh1 Negative GeneticPMID:22681890
positive genetic interaction withsac12inositol polyphosphate phosphatase (predicted) Positive GeneticPMID:22681890
negative genetic interaction withset1histone lysine methyltransferase Set1 Negative GeneticPMID:18818364
negative genetic interaction withsgf29SAGA complex subunit Sgf29 Negative GeneticPMID:18818364
negative genetic interaction withsib1ferrichrome synthetase Sib1 Negative GeneticPMID:22681890
positive genetic interaction withsil1nucleotide exchange factor for the ER lumenal Hsp70 chaperone, Sil1 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withskb5Shk1 kinase binding protein 5 Positive GeneticPMID:22681890
negative genetic interaction withsle1eisosome assembly protein Seg1 Negative GeneticPMID:22681890
negative genetic interaction withsnz1pyridoxine biosynthesis protein Negative GeneticPMID:22681890
negative genetic interaction withspa2cell polarity protein Spa2 Negative GeneticPMID:22681890
negative genetic interaction withSPAC1039.06alanine racemase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC105.02cankyrin repeat protein, implicated in meiotic cell cycle Negative GeneticPMID:22681890
positive genetic interaction withSPAC1071.05S-adenosylmethionine-dependent methyltransferase (predicted) Positive GeneticPMID:22681890
negative genetic interaction withSPAC10F6.15UPF0300 family protein 1 Negative GeneticPMID:22681890
negative genetic interaction withSPAC11D3.03cconserved protein Negative GeneticPMID:22681890
negative genetic interaction withSPAC12B10.15cribonuclease H2 complex subunit (predicted) Negative GeneticPMID:22681890
positive genetic interaction withSPAC13G6.08Cdc20/Fizzy subfamily WD repeat protein Positive GeneticPMID:22681890
negative genetic interaction withSPAC17H9.13cglutamate 5-kinase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC1A6.01chuman thyroid receptor interacting protein homolog, transcription coactivator (predicted) Negative GeneticPMID:22681890
positive genetic interaction withSPAC212.08cS. pombe specific GPI anchored protein family 1 Positive GeneticPMID:22681890
negative genetic interaction withSPAC29A4.17cmitochondrial FUN14 family protein Negative GeneticPMID:22681890
negative genetic interaction withSPAC328.04AAA family ATPase, unknown biological role Negative GeneticPMID:22681890
negative genetic interaction withSPAC4H3.06human C19orf60 homolog Negative GeneticPMID:22681890
negative genetic interaction withSPAC644.13cRab GTPase binding (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPAC750.04cS. pombe specific 5Tm protein family Negative GeneticPMID:22681890
negative genetic interaction withSPAPB1A10.05Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withSPBC1271.14glutamate N-acetyltransferase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC1709.16caromatic ring-opening dioxygenase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC409.17cDUF1769 family protein Negative GeneticPMID:22681890
negative genetic interaction withSPBC887.08Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withspf1Set1C PHD Finger protein Spf1 Negative GeneticPMID:18818364
negative genetic interaction withssr3SWI/SNF and RSC complex subunit Ssr3 Negative GeneticPMID:22681890
negative genetic interaction withsum2G2/M transition checkpoint protein Sum2 Negative GeneticPMID:18818364
negative genetic interaction withswd1Set1C complex subunit Swd1 Negative GeneticPMID:18818364
negative genetic interaction withswd3WD repeat protein Swd3 Negative GeneticPMID:22681890
positive genetic interaction withtip1CLIP170 family protein Tip1 Positive GeneticPMID:22681890
negative genetic interaction withtls1splicing factor Tls1 Negative GeneticPMID:22681890
negative genetic interaction withubp2ubiquitin C-terminal hydrolase Ubp2 Negative GeneticPMID:18818364
negative genetic interaction withubp2ubiquitin C-terminal hydrolase Ubp2 Negative GeneticPMID:22681890
negative genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:18818364
negative genetic interaction withvps1dynamin family protein Vps1 Negative GeneticPMID:22681890
phenotype enhanced byvps24ESCRT III complex subunit Vps24 Phenotypic EnhancementPMID:19547744
positive genetic interaction withvsl1vacuolar SNARE Vsl1/Vam7 Positive GeneticPMID:22681890
negative genetic interaction withyos9sensor for misfolded ER glycoproteins Yos9 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withzhf1zinc ion transmembrane transporter Zhf1 Negative GeneticPMID:22681890
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)
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
SYSGRO SPBC18H10.08c Fission yeast phenotypic data & analysis
Cyclebase SPBC18H10.08c.1 Cell Cycle Data
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:26_51 - 07 Apr 2015