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 NameCount
GTP binding113
Annotation ExtensionEvidenceWith/FromReference
GTPase activity65
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
intracellular protein transport316
Annotation ExtensionEvidenceWith/FromReference
regulation of vesicle-mediated transport22
Annotation ExtensionEvidenceWith/FromReference
small GTPase mediated signal transduction100
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2302
Annotation ExtensionEvidenceWith/FromReference
nucleus2700
Annotation ExtensionEvidenceWith/FromReference
plasma membrane253
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
slow vegetative cell population growthypt4Δ367
viable vegetative cell populationypt4Δ3850

Cell Phenotype

Term NameGenotypesCount
elongated telomeresypt4Δ176
large vacuoles present in decreased numbers during vegetative growthypt4Δ2
viable vegetative cell with normal cell morphologyypt4Δ3102

FYPO Multi-allele Phenotypes

Cell Phenotype

Term NameGenotypes
large vacuoles present in decreased numbers during salt stressypt4Δ, wis1Δ
ypt4Δ, sty1Δ
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons4950238..4949923, 4949874..4948541
Intron4949922..4949875
mRNA4950238..4948541
5' UTR4950238..4950023PMID:21511999
CDS4950022..4949923, 4949874..4949270
3' UTR4949269..4948541PMID: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
PF00071 Pfam IPR001806 Small GTPase superfamily 11 176 19
SM00175 SMART 10 178 22
SM00173 SMART 11 178 19
SM00176 SMART 15 222 13
SM00174 SMART 12 178 19
PS51419 Prosite Profiles 5 234 9
PTHR24073 HMMPANTHER 1 216 9
PTHR24073:SF450 HMMPANTHER 1 216 1
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 3 197 288
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 5 186 294
PR00449 PRINTS 55 77 19
PR00449 PRINTS 153 175 19
PR00449 PRINTS 33 49 19
PR00449 PRINTS 10 31 19
PR00449 PRINTS 117 130 19
TIGR00231 TIGRFAM IPR005225 Small GTP-binding protein domain 8 168 35

View domain organization at Pfam

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
Codon Adaptation Index 0.40
Isoelectric point 5.35
Molecular weight 26.27 kDa
Number of residues 234
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for ypt4 (SPAC1B3.11c)

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
0.34during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.18during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog600
conserved in fungi4607
conserved in eukaryotes4517
conserved in metazoa3427
conserved in vertebrates3402
conserved in eukaryotes only2502
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPAC1B3.11c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withddb1damaged DNA binding protein Ddb1 Negative GeneticPMID:22681890
negative genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withsty1MAP kinase Sty1 Negative GeneticPMID:22681890
negative genetic interaction withcph2Clr6 histone deacetylase associated PHD protein Cph2 Negative GeneticPMID:22681890
negative genetic interaction withcsn1COP9/signalosome complex subunit Csn1 Negative GeneticPMID:22681890
negative genetic interaction withtom70mitochondrial TOM complex subunit Tom70 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withsts5RNB-like protein Negative GeneticPMID:22681890
positive genetic interaction withprp4serine/threonine protein kinase Prp4 Positive GeneticPMID:22681890
positive genetic interaction withfft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive 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)
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
SYSGRO SPAC1B3.11c Fission yeast phenotypic data & analysis
Cyclebase SPAC1B3.11c.1 Cell Cycle Data
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:30_61 - 12 Sep 2016