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:0000002385
GO:0003899DNA-directed RNA polymerase activity37
contributes_to, heterologous_systemIGISGD:S000006314GO_REF:0000001
GO:0046983protein dimerization activityIEAIPR009025GO_REF:000000252
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006995cellular response to nitrogen starvationIMPPMID:1936672885
GO:0070317negative regulation of G0 to G1 transitionIMPPMID:1936672826
GO:0006360transcription from RNA polymerase I promoter29
heterologous_systemIGISGD:S000006314GO_REF:0000001
GO:0006383transcription from RNA polymerase III promoter28
heterologous_systemIGISGD:S000006314GO_REF:0000001
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005736DNA-directed RNA polymerase I complex14
heterologous_systemIGISGD:S000006314GO_REF:0000001
GO:0005666DNA-directed RNA polymerase III complex17
heterologous_systemIGISGD:S000006314GO_REF:0000001
GO:0005829cytosolIDAPMID:168233722316
GO:0005730nucleolusIDAPMID:16823372355
GO:0005634nucleusIDAPMID:168233722740
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000709decreased cell population growth during nitrogen starvationCell growth assayrpc40-410PECO:0000004, PECO:0000099PMID:1936672833
FYPO:0002061inviable vegetative cell populationMicroscopyrpc40ΔNullPMID:204732891315
Microscopyrpc40ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0000082sensitive to heatCell growth assayrpc40-410PECO:0000004, PECO:0000099PMID:19366728138

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000313inviable after spore germination, without cell division, with abnormal germ tube morphologyMicroscopyrpc40ΔNullPECO:0000005, PECO:0000137PMID:23697806144
FYPO:0002151inviable sporeMicroscopyrpc40ΔNullPECO:0000005, PECO:0000137PMID:23697806457
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 3
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 20 348 2
PTHR11800:SF13 HMMPANTHER 20 348 1
2.170.120.12 Gene3D IPR011262 DNA-directed RNA polymerase, insert domain 83 224 2
3.30.1360.10 Gene3D 41 82 4
3.30.1360.10 Gene3D 225 345 4
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)DuringConditionScaleEvidenceReference
7030.02during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
26517.9during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
42555during GO:0072690PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
42273during GO:0000084PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
46319during GO:0000080PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
41100during GO:0000087PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
44117during GO:0000085PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
3.7during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
0.45during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4569
conserved in eukaryotes4482
conserved in bacteria1001
conserved in metazoa3419
conserved in vertebrates3393
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
epe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
rpc19DNA-directed RNA polymerase I and III subunit Rpc19 Two-hybridPMID:10628857
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)
IntEnz2.7.7.6Integrated relational Enzyme database
Rhea2.7.7.6Annotated reactions database
WikiGene2539663DNA-directed RNA polymerase I and III subunit Rpc40 (predicted)
EntrezGene2539663DNA-directed RNA polymerase I and III subunit Rpc40 (predicted)
SPD / RIKEN32/32D03Orfeome Localization Data
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 (predicted)
RefSeq mRNANM_001023852972h- DNA-directed RNA polymerase I and III subunit Rpc40 (predicted) (rpc40), mRNA
European Nucleotide ArchiveAAD44503ENA Protein Mapping
European Nucleotide ArchiveAAD44503.1ENA Protein Mapping
European Nucleotide ArchiveBAA77385ENA Protein Mapping
European Nucleotide ArchiveBAA77385.1ENA Protein Mapping
European Nucleotide ArchiveCAB38687ENA Protein Mapping
European Nucleotide ArchiveCAB38687.1ENA Protein Mapping
UniParcUPI0000134603UniProt Archive

Literature for rpc40

Search: Europe PMC or PubMed

Release Version: PomBase:22_44 - 08 Jul 2014