rpb4 (SPBC337.14)


Gene Standard Namerpb4 Characterisation Statuspublished
Systematic IDSPBC337.14 Feature Typeprotein coding
Synonyms Name Description
ProductDNA-directed RNA polymerase II complex subunit Rpb4 Product Size135aa, 15.36 kDa
Genomic Location Chromosome II, 1055529-1056502 (974nt); CDS:1055662-1056226 (565nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0003899DNA-directed RNA polymerase activity37
contributes_toIDAPMID:10523639
GO:0005515protein bindingIPIrpb7PMID:10523639831
C_termIPImed8PMID:19720063
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:1900405regulation of cytokinetic cell separation by regulation of transcription from RNA polymerase II promoterIMPPMID:169720653
GO:0006366transcription from RNA polymerase II promoter335
during mitotic cell cycleIMPPMID:16972065
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0016591DNA-directed RNA polymerase II, holoenzymeIDAPMID:1052363955
GO:0005634nucleusIDAPMID:168233722740
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopynot recorded (unrecorded)PMID:105236391338
Microscopyrpb4ΔNullPMID:20473289
Cell growth assayrpb4ΔNullPMID:10523639
Microscopyrpb4ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002430inviable after spore germination, multiple cell divisionsMicroscopyrpb4ΔNullPMID:10523639210
FYPO:0002429inviable after spore germination, multiple cell divisions, abnormal cell shape, normal cell sizeMicroscopyrpb4ΔNullPECO:0000005, PECO:0000137PMID:2369780617
FYPO:0000313inviable after spore germination, without cell division, with abnormal germ tube morphologyMicroscopyrpb4ΔNullPECO:0000005, PECO:0000137PMID:23697806146
Target Of
OntologyRelationshipGeneProductReference
GO substrate of fcp1 CTD phosphatase Fcp1 PMID:11934898
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
110555291055713
210557521055857
310559031055980
410560551056502

UTRs

Region Coordinates Reference
three_prime_UTR1056227..1056502PMID: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
PF03874 Pfam IPR005574 RNA polymerase II, Rpb4 24 131 2
SM00657 SMART IPR006590 RNA polymerase II, Rpb4, core 17 134 2
PTHR21297 HMMPANTHER 2 134 1
SSF47819 SuperFamily IPR010997 HRDC-like 2 133 4

View domain organization at Pfam

Protein Properties

Ave. residue weight 113.79 Da
Charge -6.50
Isoelectric point 4.52
Molecular weight 15.36 kDa
Number of residues 135
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
35938during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
35379during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
33331during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
33113during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
3204.5during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
32107during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
7633.45during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
9.1during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Misc
DescriptionQualifierReferenceCount
deletion mutant expression profiling PMID:1697206578
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
conserved in archaea237
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
rpb3RNA polymerase II subunit 3 Affinity Capture-MSPMID:11839823
Reconstituted ComplexPMID:10648788
Co-purificationPMID:11168400
rpb1RNA polymerase II large subunit Rpb1 Affinity Capture-MSPMID:15743411
fcp1CTD phosphatase Fcp1 Affinity Capture-WesternPMID:11839823
Affinity Capture-MS
med8mediator complex subunit Med8 Reconstituted ComplexPMID:19720063
Two-hybrid
rpb7DNA-directed RNA polymerase complex II subunit Rpb7 Affinity Capture-MSPMID:16204182
Reconstituted ComplexPMID:10523639
Co-purification
Co-crystal or NMR structurePMID:15591044
set2histone lysine methyltransferase Set2 Affinity Capture-MSPMID:24583182
External References
Database Identifier Description
NBRP SPBC337.14 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC337.14 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC337.14 BioGRID Interaction Datasets
Expression Viewer SPBC337.14 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC337.14 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC337.14 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC337.14 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC337.14 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC337.14 Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC337.14 Cell Cycle Data
GEO SPBC337.14 GEO profiles
PInt SPBC337.14 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC337.14 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC337.14 Fission yeast phenotypic data & analysis
SPD / RIKEN39/39H10Orfeome Localization Data
UniProtKB/SwissProtO74825DNA-directed RNA polymerase II subunit rpb4
ModBaseO74825Database of comparative protein structure models
STRINGO74825Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595415DNA-directed RNA polymerase II complex subunit Rpb4
RefSeq mRNANM_001021322972h- DNA-directed RNA polymerase II complex subunit Rpb4 (rpb4), mRNA
European Nucleotide ArchiveAF149308ENA EMBL mapping
ePDB3H0GThe European PDB
PDB3H0GPDB
PDBsum3H0GPDBsum
European Nucleotide ArchiveBAA85621.1ENA Protein Mapping
European Nucleotide ArchiveCAA21284.1ENA Protein Mapping
UniParcUPI00001345DAUniProt Archive

Literature for rpb4

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014