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 binding868
Annotation ExtensionEvidenceWith/FromReference
binds med8
GO Biological Process
Term NameCount
transcription from RNA polymerase II promoter339
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
DNA-directed RNA polymerase II, holoenzyme55
Annotation ExtensionEvidenceWith/FromReference
nucleus2692
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationrpb4+1451
rpb4Δ

Cell Phenotype

Term NameGenotypesCount
inviable after spore germination, multiple cell divisionsrpb4Δ243
inviable after spore germination, multiple cell divisions, abnormal cell shape, normal cell sizerpb4Δ17
inviable after spore germination, without cell division, with abnormal germ tube morphologyrpb4Δ153
Target Of
OntologyRelationshipGeneProduct
GO substrate of ubp15 ubiquitin C-terminal hydrolase Ubp15
GO substrate of ubp4 ubiquitin C-terminal hydrolase Ubp4
GO substrate of ubp5 ubiquitin C-terminal hydrolase Ubp5
GO substrate of ubp9 ubiquitin C-terminal hydrolase Ubp9
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1055529..1055713, 1055752..1055857, 1055903..1055980, 1056055..1056502
Intron1055714..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 24 130 2
SM00657 SMART IPR006590 RNA polymerase II, Rpb4, core 17 134 2
PTHR21297 HMMPANTHER 7 134 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
Codon Adaptation Index 0.43
Isoelectric point 4.52
Molecular weight 15.36 kDa
Number of residues 135
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
protein leveldecreased during GO:0034605Western blot evidencePMID:11918671
decreased during GO:0009267Western blot evidencePMID:11918671
present during GO:0072690Western blot evidencePMID:11918671
decreased during GO:0060274Western blot evidencePMID:11918671

Quantitative Gene Expression

View graphical display of gene expression data for rpb4 (SPBC337.14)

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
9.1during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Misc
DescriptionQualifierReferenceCount
deletion mutant expression profiling PMID:1697206577
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in archaea238
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC337.14 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
forms complex withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Reconstituted ComplexPMID:10523639
forms complex withrpb3RNA polymerase II subunit 3 Reconstituted ComplexPMID:10648788
forms complex withmed8mediator complex subunit Med8 Reconstituted ComplexPMID:19720063
affinity captured byset2histone lysine methyltransferase Set2 Affinity Capture-MSPMID:24583182
affinity captured byrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Affinity Capture-MSPMID:16204182
affinity captured byfcp1CTD phosphatase Fcp1 Affinity Capture-WesternPMID:11839823
affinity captured byrpb3RNA polymerase II subunit 3 Affinity Capture-MSPMID:11839823
affinity captured byrpb1RNA polymerase II large subunit Rpb1 Affinity Capture-MSPMID:15743411
co-purifies withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-purificationPMID:10523639
co-purifies withrpb3RNA polymerase II subunit 3 Co-purificationPMID:11168400
binds DNA-binding domain construct withcaf4CCR4-Not complex subunit Caf4/Mdv1 (predicted) Two-hybridPMID:26771498
binds DNA-binding domain construct withSPAC26H5.02cDNA replication ATPase (predicted) Two-hybridPMID:26771498
binds DNA-binding domain construct withcbh2CENP-B homolog Cbh2 Two-hybridPMID:26771498
binds DNA-binding domain construct withcbh1kinetochore protein, CENP-B homolog Cbh1 Two-hybridPMID:26771498
binds DNA-binding domain construct withSPBC16G5.16transcription factor, zf-fungal binuclear cluster type (predicted) Two-hybridPMID:26771498
binds activation domain construct withtas3RITS complex subunit 3 Two-hybridPMID:26771498
binds activation domain construct withmed8mediator complex subunit Med8 Two-hybridPMID:19720063
co-locates (via crystalisation or NMR) withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-crystal or NMR structurePMID:15591044
affinity capturesfcp1CTD phosphatase Fcp1 Affinity Capture-WesternPMID:11839823
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

Literature for rpb4

Search: Europe PMC or PubMed

Release Version: PomBase:30_59 - 12 Apr 2016