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 binding887
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:169720654
GO:0006366transcription from RNA polymerase II promoter130
during mitotic cell cycleIMPPMID:16972065
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0016591DNA-directed RNA polymerase II, holoenzymeTASPMID:1052363954
GO:0005634nucleusIDAPMID:168233722730
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationno_namePMID:105236391309
Microscopyrpb4ΔNullPECO:0000005, PECO:0000137PMID:23697806
Microscopyrpb4ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
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:23697806144
Target Of
RelationshipGeneProductReference
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 Start End Reference
three_prime_UTR10562271056502PMID: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 1
PTHR21297 HMMPANTHER 2 134 1
SSF47819 SuperFamily IPR010997 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)DuringConditionScaleEvidenceReference
3204.5during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
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)DuringConditionScaleEvidenceReference
2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
9.1during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
Misc
DescriptionQualifierReferenceCount
deletion mutant expression profiling PMID:1697206579
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in archaea237
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
fcp1CTD phosphatase Fcp1 Affinity Capture-WesternPMID:11839823
Affinity Capture-MS
rpb7DNA-directed RNA polymerase complex II subunit Rpb7 Affinity Capture-MSPMID:16204182
Co-purificationPMID:10523639
Reconstituted Complex
Co-crystal StructurePMID:15591044
med8mediator complex subunit Med8 Reconstituted ComplexPMID:19720063
Two-hybrid
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
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)
SPD / RIKEN39/39H10Orfeome Localization Data
WikiGene2541011DNA-directed RNA polymerase II complex subunit Rpb4
EntrezGene2541011DNA-directed RNA polymerase II complex subunit Rpb4
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
ePDB3H0GThe European PDB
PDBsum3H0GPDBsum
European Nucleotide ArchiveAAF62856ENA Protein Mapping
European Nucleotide ArchiveBAA85621ENA Protein Mapping
European Nucleotide ArchiveCAA21284ENA Protein Mapping
UniParcUPI00001345DAUniProt Archive

Literature for rpb4

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014