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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0030433ER-associated ubiquitin-dependent protein catabolic processISSUniProtKB:Q05787GO_REF:000000126
GO:0016567protein ubiquitinationNASGO_REF:0000051115
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005783endoplasmic reticulumIDAPMID:16823372594
GO:0005789endoplasmic reticulum membraneISSUniProtKB:Q05787GO_REF:0000001207
GO:0016021integral component of membraneIEAUniProtKB-KW:KW-0812GO_REF:00000371016
GO:0000151ubiquitin ligase complexNASGO_REF:000005160
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001701sensitive to bortezomibCell growth assaySPBC28F2.08cΔNullPECO:0000005, PECO:0000137PMID:21760946256
expressivity FYPO_EXT:0000002
FYPO:0002060viable vegetative cell populationMicroscopySPBC28F2.08cΔNullPECO:0000005, PECO:0000137PMID:236978063755
MicroscopySPBC28F2.08cΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphologyMicroscopySPBC28F2.08cΔNullPECO:0000005, PECO:0000137PMID:236978063078
penetrance FYPO_EXT:0000001
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
115843201581815

UTRs

Region Start End Reference
five_prime_UTR15843201584245PMID:21511999
three_prime_UTR15821021581815PMID: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 474 489 6
PF08238 Pfam IPR006597 Sel1-like 281 314 6
PF08238 Pfam IPR006597 Sel1-like 495 522 6
PF08238 Pfam IPR006597 Sel1-like 83 123 6
PF08238 Pfam IPR006597 Sel1-like 527 554 6
PF08238 Pfam IPR006597 Sel1-like 215 243 6
PF08238 Pfam IPR006597 Sel1-like 127 157 6
SM00671 SMART IPR006597 Sel1-like 83 124 7
SM00671 SMART IPR006597 Sel1-like 125 160 7
SM00671 SMART IPR006597 Sel1-like 280 315 7
SM00671 SMART IPR006597 Sel1-like 212 248 7
SM00671 SMART IPR006597 Sel1-like 527 562 7
SM00671 SMART IPR006597 Sel1-like 490 525 7
TMhelix TMHMM 673 690 959
PTHR11102 HMMPANTHER 21 712 7
PTHR11102:SF1 HMMPANTHER 21 712 1
G3DSA:1.25.40.10 Gene3D IPR011990 473 562 55
G3DSA:1.25.40.10 Gene3D IPR011990 76 158 55
G3DSA:1.25.40.10 Gene3D IPR011990 193 370 55
SSF81901 SuperFamily 281 400 9
SSF81901 SuperFamily 78 158 9
SSF81901 SuperFamily 458 561 9
SSF81901 SuperFamily 210 246 9
SignalP-noTM signalp 1 19 212
Low complexity (SEG) seg 692 712
Low complexity (SEG) seg 679 690
Low complexity (SEG) seg 3 14

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_peptide278
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)DuringConditionScaleEvidenceReference
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
1039.54during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
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)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in eukaryotes only2485
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
ams2cell cycle regulated GATA-type transcription factor Ams2 Negative GeneticPMID:22681890
cdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
SPAC821.05translation initiation factor eIF3h (p40) Negative GeneticPMID:22681890
rad55RecA family ATPase Rad55/Rhp55 Negative GeneticPMID:22681890
SPCC162.11curidine kinase/uracil phosphoribosyltransferase (predicted) Negative GeneticPMID:22681890
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:22681890
SPCC1322.02sequence orphan Negative GeneticPMID:22681890
SPBC29A3.09cAAA family ATPase Gcn20 (predicted) Positive GeneticPMID:22681890
rad57RecA family ATPase Rad57/Rhp57 Negative GeneticPMID:22681890
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)
WikiGene2540568HRD ubiquitin ligase complex subunit (predicted)
EntrezGene2540568HRD ubiquitin ligase complex subunit (predicted)
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 ArchiveBAA12178ENA Protein Mapping
European Nucleotide ArchiveBAA12179ENA Protein Mapping
European Nucleotide ArchiveCAB57937ENA Protein Mapping
UniParcUPI000006BA3BUniProt Archive

Literature for SPBC28F2.08c

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014