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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0006896Golgi to vacuole transportISOSGD:S000003566GO_REF:000002418
GO:0006886intracellular protein transportICGO:0042147GO_REF:0000001338
GO:0042147retrograde transport, endosome to GolgiISOSGD:S000003566GO_REF:000002423
GO:0016192vesicle-mediated transportISOSGD:S000003566GO_REF:0000024320
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0000938GARP complexISOSGD:S000003566GO_REF:00000244
GO:0005737cytoplasmIDAPMID:168233724205
GO:0005768endosomeIEAUniProtKB-KW:KW-0967GO_REF:000003777
GO:0016020membraneIEAUniProtKB-KW:KW-0472GO_REF:00000371454
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyvps53ΔNullPECO:0000005, PECO:0000137PMID:236978061338
Microscopyvps53ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002451inviable vegetative cell with abnormal cell shapeMicroscopyvps53ΔNullPECO:0000005, PECO:0000137PMID:23697806460
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
114464801449286

UTRs

Region Coordinates Reference
five_prime_UTR1446480..1446702PMID:21511999
three_prime_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:SF0 HMMPANTHER 18 712 1
PTHR12820 HMMPANTHER 18 712 1
Coil ncoils Rabaptin coiled-coil domain 46 67 968

View domain organization at Pfam

Protein Properties

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

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
5163during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
5694during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
5018during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
5158during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
643.36during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
5419during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
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
1.4during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.35during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
conserved in eukaryotes only2497
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)
Cyclebase SPAC3A12.15 Cell Cycle Data
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
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
European Nucleotide ArchiveCAB08743.1ENA Protein Mapping
UniParcUPI000013AA01UniProt Archive

Literature for vps53

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014