SPBC28F2.08c


Gene Standard NameUnassigned Characterisation Statusbiological_role_inferred
Systematic IDSPBC28F2.08c Feature Typeprotein coding
Synonyms Name Description
ProductHRD ubiquitin ligase complex subunit (predicted) Product Size713aa, 80.26 kDa
Genomic Location Chromosome II, 1584320-1581815 (2506nt); CDS:1584244-1582103 (2142nt)

Ensembl Gene Location
GO Biological Process
Term NameCount
ER-associated ubiquitin-dependent protein catabolic process28
Annotation ExtensionEvidenceWith/FromReference
protein ubiquitination117
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
endoplasmic reticulum596
Annotation ExtensionEvidenceWith/FromReference
endoplasmic reticulum membrane205
Annotation ExtensionEvidenceWith/FromReference
integral component of membrane1018
Annotation ExtensionEvidenceWith/FromReference
ubiquitin ligase complex60
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
sensitive to bortezomibSPBC28F2.08cΔNull256
viable vegetative cell populationSPBC28F2.08cΔNull3792

Cell Phenotype

Term NameAlleleExpressionCount
viable vegetative cell with normal cell morphologySPBC28F2.08cΔNull3092
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1584320..1581815
mRNA1584320..1581815
5' UTR1584320..1584245PMID:21511999
CDS1584244..1582103
3' UTR1582102..1581815PMID: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
PF08238 Pfam IPR006597 Sel1-like 281 314 6
PF08238 Pfam IPR006597 Sel1-like 127 157 6
PF08238 Pfam IPR006597 Sel1-like 527 554 6
PF08238 Pfam IPR006597 Sel1-like 474 489 6
PF08238 Pfam IPR006597 Sel1-like 83 123 6
PF08238 Pfam IPR006597 Sel1-like 215 243 6
PF08238 Pfam IPR006597 Sel1-like 495 522 6
SM00671 SMART IPR006597 Sel1-like 212 248 7
SM00671 SMART IPR006597 Sel1-like 527 562 7
SM00671 SMART IPR006597 Sel1-like 490 525 7
SM00671 SMART IPR006597 Sel1-like 125 160 7
SM00671 SMART IPR006597 Sel1-like 280 315 7
SM00671 SMART IPR006597 Sel1-like 83 124 7
TMhelix TMHMM 673 690 959
PTHR11102 HMMPANTHER 73 680 7
PTHR11102:SF56 HMMPANTHER 73 680 1
1.25.40.10 Gene3D IPR011990 Tetratricopeptide-like helical domain 193 370 62
1.25.40.10 Gene3D IPR011990 Tetratricopeptide-like helical domain 473 562 62
1.25.40.10 Gene3D IPR011990 Tetratricopeptide-like helical domain 76 158 62
SSF81901 SuperFamily 210 246 9
SSF81901 SuperFamily 458 561 9
SSF81901 SuperFamily 78 158 9
SSF81901 SuperFamily 281 400 9
SignalP-noTM signalp 1 19 212

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000212SEL1 repeat proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000212

Sequence Ontology

Term IDTerm NameReferenceCount
SO:0000418signal_peptide279
SO:0001812transmembrane_helix465

Protein Properties

Ave. residue weight 112.57 Da
Charge 10.00
Isoelectric point 7.57
Molecular weight 80.26 kDa
Number of residues 713
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2413during GO:0000080PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
2272during GO:0000084PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
2313during GO:0000085PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
2482during GO:0000087PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
2269during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
1039.54during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
5.8during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
1.7during 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 fungi4604
conserved in eukaryotes4516
conserved in metazoa3430
conserved in vertebrates3405
conserved in eukaryotes only2502
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withams2cell cycle regulated GATA-type transcription factor Ams2 Negative GeneticPMID:22681890
negative genetic interaction withcdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
positive genetic interaction withgcn20AAA family ATPase Gcn20 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withpxd1structure-specific DNA nuclease regulator Pxd1 Negative GeneticPMID:22681890
negative genetic interaction withrad55RecA family ATPase Rad55/Rhp55 Negative GeneticPMID:22681890
negative genetic interaction withrad57RecA family ATPase Rad57/Rhp57 Negative GeneticPMID:22681890
positive genetic interaction withsgf73SAGA complex subunit Sgf73 Positive GeneticPMID:25076038
negative genetic interaction withSPCC162.11curidine kinase/uracil phosphoribosyltransferase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withtif38translation initiation factor eIF3h (p40) Negative GeneticPMID:22681890
positive genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:22681890
negative genetic interaction withxap5xap-5-like protein Negative GeneticPMID:24957674
External References
Database Identifier Description
NBRP SPBC28F2.08c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC28F2.08c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC28F2.08c BioGRID Interaction Datasets
Expression Viewer SPBC28F2.08c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC28F2.08c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC28F2.08c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC28F2.08c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC28F2.08c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC28F2.08c Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC28F2.08c Cell Cycle Data
GEO SPBC28F2.08c GEO profiles
PInt SPBC28F2.08c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC28F2.08c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC28F2.08c Fission yeast phenotypic data & analysis
SPD / RIKEN37/37E08Orfeome Localization Data
UniProtKB/SwissProtQ9USV0Putative ERAD-associated E3 ubiquitin-protein ligase component
ModBaseQ9USV0Database of comparative protein structure models
STRINGQ9USV0Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595669HRD ubiquitin ligase complex subunit (predicted)
RefSeq mRNANM_001021564972h- HRD ubiquitin ligase complex subunit (predicted) (SPBC28F2.08c), mRNA
European Nucleotide ArchiveBAA12178.1ENA Protein Mapping
European Nucleotide ArchiveBAA12179.1ENA Protein Mapping
European Nucleotide ArchiveCAB57937.1ENA Protein Mapping
UniParcUPI000006BA3BUniProt Archive

Literature for SPBC28F2.08c

Search: Europe PMC or PubMed

Release Version: PomBase:25_50 - 10 Mar 2015