vps53 (SPAC3A12.15)


Gene Standard Namevps53 Characterisation Statusbiological role inferred
Systematic IDSPAC3A12.15 Feature Typeprotein coding
Synonyms Name Description
ProductGARP complex subunit Vps53 (predicted) Product Size756aa, 87.51 kDa
Genomic Location Chromosome I, 1446480-1449286 (2807nt); CDS:1446703-1448973 (2271nt)

Ensembl Gene Location
GO Biological Process
Term NameCount
Golgi to vacuole transport18
Annotation ExtensionEvidenceWith/FromReference
intracellular protein transport333
Annotation ExtensionEvidenceWith/FromReference
retrograde transport, endosome to Golgi23
Annotation ExtensionEvidenceWith/FromReference
vesicle-mediated transport322
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytoplasm4211
Annotation ExtensionEvidenceWith/FromReference
endosome80
Annotation ExtensionEvidenceWith/FromReference
GARP complex4
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationvps53Δ1451

Cell Phenotype

Term NameGenotypesCount
inviable vegetative cell with abnormal cell shapevps53Δ770
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1446480..1449286
mRNA1446480..1449286
5' UTR1446480..1446702PMID:21511999
CDS1446703..1448973
3' UTR1448974..1449286PMID: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
PF04100 Pfam IPR007234 Vps53-like, N-terminal 17 393 1
PTHR12820 HMMPANTHER 18 722 1
PTHR12820:SF0 HMMPANTHER 18 722 1
Coil ncoils Predicted coiled-coil protein (DUF2205) 46 66 1057

View domain organization at Pfam

Protein Properties

Ave. residue weight 115.75 Da
Charge 4.00
Codon Adaptation Index 0.40
Isoelectric point 7.55
Molecular weight 87.51 kDa
Number of residues 756
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for vps53 (SPAC3A12.15)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
5163during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
5694during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
5018during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
5158during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
643.36during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
5419during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.4during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.35during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2506
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


External References
Database Identifier Description
NBRP SPAC3A12.15 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC3A12.15 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC3A12.15 BioGRID Interaction Datasets
Expression Viewer SPAC3A12.15 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC3A12.15 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC3A12.15 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC3A12.15 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC3A12.15 Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC3A12.15 Transcriptome Viewer (Bähler Lab)
GEO SPAC3A12.15 GEO profiles
PInt SPAC3A12.15 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC3A12.15 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC3A12.15 Fission yeast phenotypic data & analysis
Cyclebase SPAC3A12.15.1 Cell Cycle Data
SPD / RIKEN28/28B07Orfeome Localization Data
UniProtKB/SwissProtP87129Vacuolar protein sorting-associated protein 53
ModBaseP87129Database of comparative protein structure models
STRINGP87129Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593341GARP complex subunit Vps53 (predicted)
RefSeq mRNANM_001018773972h- GARP complex subunit Vps53 (predicted) (vps53), mRNA

Literature for vps53

Search: Europe PMC or PubMed

Release Version: PomBase:30_59 - 12 Apr 2016