hrd3 (SPBC28F2.08c)


Gene Standard Namehrd3 Characterisation Statusbiological role inferred
Systematic IDSPBC28F2.08c Feature Typeprotein coding
Synonyms Name Description
ProductHrd1 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
GO Cellular Component
Term NameCount
endoplasmic reticulum599
Annotation ExtensionEvidenceWith/FromReference
endoplasmic reticulum membrane204
Annotation ExtensionEvidenceWith/FromReference
Hrd1p ubiquitin ligase complex9
Annotation ExtensionEvidenceWith/FromReference
integral component of membrane966
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
sensitive to bortezomibhrd3Δ255
viable vegetative cell populationhrd3Δ3850

Cell Phenotype

Term NameGenotypesCount
decreased misfolded glycoprotein degradationhrd3Δ5
increased pre-mRNA level87
affecting fet5hrd3Δ
viable vegetative cell with normal cell morphologyhrd3Δ3102
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in hrd1 Hrd1 ubiquitin ligase complex synviolin family ubiquitin-protein ligase E3 subunit, Hrd1
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 repeat 126 156 6
PF08238 Pfam IPR006597 Sel1-like repeat 213 244 6
PF08238 Pfam IPR006597 Sel1-like repeat 528 555 6
PF08238 Pfam IPR006597 Sel1-like repeat 492 522 6
PF08238 Pfam IPR006597 Sel1-like repeat 83 123 6
PF08238 Pfam IPR006597 Sel1-like repeat 281 314 6
PF08238 Pfam IPR006597 Sel1-like repeat 472 489 6
SM00671 SMART IPR006597 Sel1-like repeat 83 124 7
SM00671 SMART IPR006597 Sel1-like repeat 490 525 7
SM00671 SMART IPR006597 Sel1-like repeat 125 160 7
SM00671 SMART IPR006597 Sel1-like repeat 212 248 7
SM00671 SMART IPR006597 Sel1-like repeat 280 315 7
SM00671 SMART IPR006597 Sel1-like repeat 527 562 7
TMhelix TMHMM 673 690 950
PTHR11102 HMMPANTHER 434 583 7
PTHR11102:SF81 HMMPANTHER 75 155 1
PTHR11102:SF81 HMMPANTHER 207 245 1
PTHR11102:SF81 HMMPANTHER 276 391 1
PTHR11102:SF81 HMMPANTHER 434 583 1
PTHR11102 HMMPANTHER 75 155 7
PTHR11102 HMMPANTHER 207 245 7
PTHR11102 HMMPANTHER 276 391 7
1.25.40.10 Gene3D IPR011990 Tetratricopeptide-like helical domain 473 562 62
1.25.40.10 Gene3D IPR011990 Tetratricopeptide-like helical domain 193 370 62
1.25.40.10 Gene3D IPR011990 Tetratricopeptide-like helical domain 76 158 62
SSF81901 SuperFamily 458 561 9
SSF81901 SuperFamily 78 158 9
SSF81901 SuperFamily 210 246 9
SSF81901 SuperFamily 281 400 9
SignalP-noTM signalp 1 19 207

View domain organization at Pfam

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

Term IDTerm NameReferenceCount
SO:0000418signal_peptide279
SO:0001812transmembrane_helix465

Protein Properties

Ave. residue weight 112.57 Da
Charge 10.00
Codon Adaptation Index 0.37
Isoelectric point 7.57
Molecular weight 80.26 kDa
Number of residues 713
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for hrd3 (SPBC28F2.08c)

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
5.8during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1.7during 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)3093
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 SPBC28F2.08c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withxap5xap-5-like protein Negative GeneticPMID:24957674
negative genetic interaction withpxd1structure-specific DNA nuclease regulator Pxd1 Negative GeneticPMID:22681890
negative genetic interaction withtif38translation initiation factor eIF3h (p40) Negative GeneticPMID:22681890
negative genetic interaction withurk1uridine kinase/uracil phosphoribosyltransferase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withrad55RecA family ATPase Rad55/Rhp55 Negative GeneticPMID:22681890
negative genetic interaction withams2cell cycle regulated GATA-type transcription factor Ams2 Negative GeneticPMID:22681890
negative genetic interaction withrad57RecA family ATPase Rad57/Rhp57 Negative GeneticPMID:22681890
negative genetic interaction withcdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
positive genetic interaction withgcn20AAA family ATPase Gcn20 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withsgf73SAGA complex subunit Sgf73 Positive GeneticPMID:25076038
positive genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive 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)
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
Cyclebase SPBC28F2.08c.1 Cell Cycle Data
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 hrd3

Search: Europe PMC or PubMed

Release Version: PomBase:30_61 - 12 Sep 2016