ypt4 (SPAC1B3.11c)


Gene Standard Nameypt4 Characterisation Statuspublished
Systematic IDSPAC1B3.11c Feature Typeprotein coding
Synonyms Name Description
ProductGTPase Ypt4 Product Size234aa, 26.27 kDa
Genomic Location Chromosome I, 4950238-4948541 (1698nt); CDS:4950022-4949270 (753nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005525GTP bindingIEAUniProtKB-KW:KW-0342GO_REF:0000037113
GO:0003924GTPase activityISMPFAM:PF00071GO_REF:000000161
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006184GTP catabolic processISMPFAM:PF00071GO_REF:000000148
GO:0006886intracellular protein transportICGO:0016192GO_REF:0000001326
GO:0060627regulation of vesicle-mediated transportISMPFAM:PF00071GO_REF:000000126
GO:0007264small GTPase mediated signal transductionIEAIPR001806GO_REF:000000263
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005829cytosolIDAPMID:168233722319
GO:0005634nucleusIDAPMID:168233722737
GO:0005886plasma membraneIEAUniProtKB-KW:KW-1003GO_REF:0000037244
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002060viable vegetative cell populationMicroscopyypt4ΔNullPECO:0000005, PECO:0000137PMID:236978063751
Microscopyypt4ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002019elongated telomeres157
expressivity FYPO_EXT:0000003Gel electrophoresis evidenceypt4ΔNullPMID:20625380
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001Microscopyypt4ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
149502384949923
249498744948541
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
PF00071 Pfam IPR001806 Small GTPase superfamily 11 176 18
SM00173 SMART IPR020849 Small GTPase superfamily, Ras type 11 178 19
SM00174 SMART IPR003578 Small GTPase superfamily, Rho type 12 178 19
SM00175 SMART IPR003579 Small GTPase superfamily, Rab type 10 178 22
SM00176 SMART IPR002041 Ran GTPase 15 222 13
PS51419 Prosite Profiles 5 234 9
PTHR24073:SF185 HMMPANTHER 3 202 1
PTHR24073 HMMPANTHER 3 202 9
3.40.50.300 Gene3D 3 197 288
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 5 186 294
PR00449 PRINTS IPR001806 Small GTPase superfamily 55 77 19
PR00449 PRINTS IPR001806 Small GTPase superfamily 117 130 19
PR00449 PRINTS IPR001806 Small GTPase superfamily 10 31 19
PR00449 PRINTS IPR001806 Small GTPase superfamily 153 175 19
PR00449 PRINTS IPR001806 Small GTPase superfamily 33 49 19
TIGR00231 tigrfam IPR005225 Small GTP-binding protein domain 8 168 35

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0001421Ypt subfamilyTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001421

Protein Properties

Ave. residue weight 112.26 Da
Charge -3.00
Isoelectric point 5.35
Molecular weight 26.27 kDa
Number of residues 234
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
NDduring 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
0.34during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.18during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog601
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
prp4serine/threonine protein kinase Prp4 Positive GeneticPMID:22681890
ddb1damaged DNA binding protein Ddb1 Negative GeneticPMID:22681890
tom70mitochondrial TOM complex subunit Tom70 (predicted) Negative GeneticPMID:22681890
fft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:22681890
ccr4CCR4-Not complex subunit Ccr4 (predicted) Negative GeneticPMID:22681890
cph2Clr6 histone deacetylase associated PHD protein-2 Cph2 Negative GeneticPMID:22681890
sts5RNB-like protein Negative GeneticPMID:22681890
csn1COP9/signalosome complex subunit Csn1 Negative GeneticPMID:22681890
sty1MAP kinase Sty1 Negative GeneticPMID:22681890
External References
Database Identifier Description
NBRP SPAC1B3.11c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC1B3.11c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC1B3.11c BioGRID Interaction Datasets
Expression Viewer SPAC1B3.11c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC1B3.11c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC1B3.11c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC1B3.11c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC1B3.11c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC1B3.11c Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC1B3.11c Cell Cycle Data
GEO SPAC1B3.11c GEO profiles
PInt SPAC1B3.11c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC1B3.11c Peptides identified in tandem mass spectrometry proteomics experiments
SPD / RIKEN43/43B04Orfeome Localization Data
UniProtKB/SwissProtO13876GTP-binding protein ypt4
ModBaseO13876Database of comparative protein structure models
STRINGO13876Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_594796GTPase Ypt4
RefSeq mRNANM_001020224972h- GTPase Ypt4 (ypt4), mRNA
European Nucleotide ArchiveCAB11239.1ENA Protein Mapping
UniParcUPI000013BE3EUniProt Archive

Literature for ypt4

Search: Europe PMC or PubMed

Release Version: PomBase:23_46 - 30 Aug 2014