rpc40 (SPBC1289.07c)


Gene Standard Namerpc40 Characterisation Statuspublished
Systematic IDSPBC1289.07c Feature Typeprotein coding
Synonymsrpa42 Name Description
ProductDNA-directed RNA polymerase I and III subunit Rpc40 Product Size348aa, 39.15 kDa
Genomic Location Chromosome II, 4397207-4395913 (1295nt); CDS:4397099-4396053 (1047nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0003677DNA bindingIEAIPR001514GO_REF:0000002383
GO:0001054RNA polymerase I activity2
contributes_to, heterologous_systemIGISGD:S000006314PMID:10628857
GO:0001056RNA polymerase III activity2
contributes_to, heterologous_systemIGISGD:S000006314PMID:10628857
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006995cellular response to nitrogen starvationIMPPMID:1936672886
GO:0006360transcription from RNA polymerase I promoter34
heterologous_systemIGISGD:S000006314PMID:10628857
GO:0006383transcription from RNA polymerase III promoter32
heterologous_systemIGISGD:S000006314PMID:10628857
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005736DNA-directed RNA polymerase I complex14
heterologous_systemIGISGD:S000006314PMID:10628857
GO:0005666DNA-directed RNA polymerase III complex17
heterologous_systemIGISGD:S000006314PMID:10628857
GO:0005829cytosolIDAPMID:168233722315
GO:0005730nucleolusIDAPMID:16823372343
GO:0005634nucleusIDAPMID:168233722740
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000082decreased cell population growth at high temperatureCell growth assayrpc40-410PECO:0000004, PECO:0000099PMID:19366728148
FYPO:0000709decreased cell population growth during nitrogen starvationCell growth assayrpc40-410PECO:0000004, PECO:0000099PMID:1936672835
FYPO:0002059inviable cell populationCell growth assayrpc40ΔNullPMID:106288571343
FYPO:0002061inviable vegetative cell populationMicroscopyrpc40ΔNullPMID:204732891338
Microscopyrpc40ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000313inviable after spore germination, without cell division, with abnormal germ tube morphologyMicroscopyrpc40ΔNullPECO:0000005, PECO:0000137PMID:23697806146
FYPO:0002151inviable sporeMicroscopyrpc40ΔNullPECO:0000005, PECO:0000137PMID:23697806465
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
143972074395913

UTRs

Region Coordinates Reference
five_prime_UTR4397207..4397100PMID:21511999
three_prime_UTR4396052..4395913PMID: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
PF01193 Pfam IPR009025 DNA-directed RNA polymerase, RBP11-like dimerisation domain 59 335 2
PF01000 Pfam IPR011262 DNA-directed RNA polymerase, insert domain 89 227 2
SM00662 SMART IPR011263 DNA-directed RNA polymerase, RpoA/D/Rpb3-type 57 341 2
PS00446 Prosite Patterns IPR001514 DNA-directed RNA polymerase, 30-40kDa subunit, conserved site 71 111 2
PTHR11800 HMMPANTHER 39 348 2
PTHR11800:SF13 HMMPANTHER 39 348 1
3.30.1360.10 Gene3D 225 345 4
3.30.1360.10 Gene3D 41 82 4
2.170.120.12 Gene3D IPR011262 DNA-directed RNA polymerase, insert domain 83 224 2
SSF55257 SuperFamily IPR009025 DNA-directed RNA polymerase, RBP11-like dimerisation domain 255 344 4
SSF55257 SuperFamily IPR009025 DNA-directed RNA polymerase, RBP11-like dimerisation domain 44 87 4
SSF56553 SuperFamily IPR011262 DNA-directed RNA polymerase, insert domain 82 228 2

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.51 Da
Charge -6.00
Isoelectric point 5.31
Molecular weight 39.15 kDa
Number of residues 348
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
46319during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
42273during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
44117during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
41100during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
42555during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
26517.9during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
7030.02during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3.7during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.45during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Complementation
DescriptionQualifierReference
functionally complements S. cerevisiae RPC40full PMID:10628857
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in bacteria1000
conserved in metazoa3425
conserved in vertebrates3400
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
mtl1TRAMP complex ATP-dependent RNA helicase (predicted) Affinity Capture-MSPMID:24713849
pir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
epe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
red1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
rpc19DNA-directed RNA polymerase I and III subunit Rpc19 Two-hybridPMID:10628857
red5human ZC3H3 homolog Affinity Capture-MSPMID:24713849
External References
Database Identifier Description
NBRP SPBC1289.07c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC1289.07c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC1289.07c BioGRID Interaction Datasets
Expression Viewer SPBC1289.07c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC1289.07c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC1289.07c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC1289.07c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC1289.07c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC1289.07c Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC1289.07c Cell Cycle Data
GEO SPBC1289.07c GEO profiles
PInt SPBC1289.07c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC1289.07c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC1289.07c Fission yeast phenotypic data & analysis
SPD / RIKEN32/32D03Orfeome Localization Data
IntEnz2.7.7.6Integrated relational Enzyme database
Rhea2.7.7.6Annotated reactions database
UniProtKB/SwissProtO94616DNA-directed RNA polymerases I and III subunit RPAC1
ModBaseO94616Database of comparative protein structure models
STRINGO94616Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596831DNA-directed RNA polymerase I and III subunit Rpc40
RefSeq mRNANM_001023852972h- DNA-directed RNA polymerase I and III subunit Rpc40 (rpc40), mRNA
European Nucleotide ArchiveAAD44503.1ENA Protein Mapping
European Nucleotide ArchiveBAA77385.1ENA Protein Mapping
European Nucleotide ArchiveCAB38687.1ENA Protein Mapping
UniParcUPI0000134603UniProt Archive

Literature for rpc40

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014