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 NameCount
DNA-directed RNA polymerase activity37
Annotation ExtensionEvidenceWith/FromReference
protein binding859
Annotation ExtensionEvidenceWith/FromReference
binds med8
GO Biological Process
Term NameCount
transcription from RNA polymerase II promoter333
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
DNA-directed RNA polymerase II, holoenzyme55
Annotation ExtensionEvidenceWith/FromReference
nucleus2696
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term NameAlleleExpressionCount
inviable vegetative cell populationrpb4+ (wild type)Knockdown1438
rpb4ΔNull
unnamed (unrecorded)

Cell Phenotype

Term NameAlleleExpressionCount
inviable after spore germination, multiple cell divisionsrpb4ΔNull229
inviable after spore germination, multiple cell divisions, abnormal cell shape, normal cell sizerpb4ΔNull17
inviable after spore germination, without cell division, with abnormal germ tube morphologyrpb4ΔNull153
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1055529..1055713, 1055752..1055857, 1055903..1055980, 1056055..1056502
Introns1055714..1055751, 1055858..1055902, 1055981..1056054
mRNA1055529..1056502
5' UTR1055529..1055661AU006882
CDS1055662..1055713, 1055752..1055857, 1055903..1055980, 1056055..1056226
3' 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
32107during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
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)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:1697206577
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4603
conserved in eukaryotes4514
conserved in metazoa3424
conserved in vertebrates3399
conserved in archaea238
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured byfcp1CTD phosphatase Fcp1 Affinity Capture-MSPMID:11839823
affinity captured byfcp1CTD phosphatase Fcp1 Affinity Capture-WesternPMID:11839823
affinity capturesfcp1CTD phosphatase Fcp1 Affinity Capture-WesternPMID:11839823
forms complex withmed8mediator complex subunit Med8 Reconstituted ComplexPMID:19720063
binds activation domain construct withmed8mediator complex subunit Med8 Two-hybridPMID:19720063
affinity captured byrpb1RNA polymerase II large subunit Rpb1 Affinity Capture-MSPMID:15743411
affinity captured byrpb3RNA polymerase II subunit 3 Affinity Capture-MSPMID:11839823
forms complex withrpb3RNA polymerase II subunit 3 Reconstituted ComplexPMID:10648788
co-purifies withrpb3RNA polymerase II subunit 3 Co-purificationPMID:11168400
affinity captured byrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Affinity Capture-MSPMID:16204182
forms complex withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Reconstituted ComplexPMID:10523639
co-purifies withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-purificationPMID:10523639
rpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-crystal or NMR structurePMID:15591044
affinity captured byset2histone 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)
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
Cyclebase SPBC337.14.1 Cell Cycle Data
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:26_53 - 27 May 2015