rpb9 (SPAPYUG7.04c)


Gene Standard Namerpb9 Characterisation Statuspublished
Systematic IDSPAPYUG7.04c Feature Typeprotein coding
Synonyms Name Description
ProductDNA-directed RNA polymerase II complex subunit Rpb9 Product Size113aa, 13.17 kDa
Genomic Location Chromosome I, 4752521-4751390 (1132nt); CDS:4752332-4751684 (649nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
DNA binding373
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase activity37
Annotation ExtensionEvidenceWith/FromReference
zinc ion binding238
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
transcription from RNA polymerase II promoter336
Annotation ExtensionEvidenceWith/FromReference
transcription-coupled nucleotide-excision repair7
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2306
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase II, core complex11
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase II, holoenzyme55
Annotation ExtensionEvidenceWith/FromReference
nucleolus366
Annotation ExtensionEvidenceWith/FromReference
nucleus2690
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
normal growth on sodium butyraterpb9Δ55
normal growth on trichostatin Arpb9Δ114
sensitive to 5-fluorouracilrpb9Δ273
sensitive to valproic acidrpb9Δ155
viable vegetative cell populationrpb9Δ3831

Cell Phenotype

Term NameGenotypesCount
viable vegetative cell with normal cell morphologyrpb9Δ3099
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons4752521..4752292, 4752224..4752158, 4752034..4751985, 4751942..4751810, 4751734..4751390
Intron4752291..4752225, 4752157..4752035, 4751984..4751943, 4751809..4751735
5' UTR4752521..4752333PMID:21511999
3' UTR4751683..4751390PMID: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
PF02150 Pfam IPR001529 DNA-directed RNA polymerase, M/15kDa subunit 4 36 3
PF01096 Pfam IPR001222 Zinc finger, TFIIS-type 74 110 4
SM00440 SMART IPR001222 Zinc finger, TFIIS-type 73 112 4
SM00661 SMART IPR001529 DNA-directed RNA polymerase, M/15kDa subunit 5 58 3
PS00466 Prosite Patterns IPR001222 Zinc finger, TFIIS-type 75 110 3
PS01030 Prosite Patterns IPR019761 DNA-directed RNA polymerase M, 15kDa subunit, conserved site 6 32 3
PS51133 Prosite Profiles IPR001222 Zinc finger, TFIIS-type 71 111 4
PTHR11239:SF1 HMMPANTHER 1 113 1
PTHR11239 HMMPANTHER 1 113 3
2.20.25.10 Gene3D Transcription elongation factor S-IIM 1 46 7
2.20.25.10 Gene3D Transcription elongation factor S-IIM 51 112 7
SSF57783 SuperFamily 1 48 8
SSF57783 SuperFamily 54 112 8
PIRSF005586 PIRSF IPR012164 DNA-directed RNA polymerase, subunit C11/M/9 4 113 3

View domain organization at Pfam

Protein Properties

Ave. residue weight 116.59 Da
Charge -1.00
Codon Adaptation Index 0.41
Isoelectric point 6.22
Molecular weight 13.17 kDa
Number of residues 113
Sequence
Gene Expression

Qualitative Gene Expression

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

Quantitative Gene Expression

View graphical display of gene expression data for rpb9 (SPAPYUG7.04c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
7147.16during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
3957.79during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
5.2during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1.2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3090
conserved in fungi4604
conserved in eukaryotes4514
conserved in metazoa3422
conserved in vertebrates3397
conserved in archaea238
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Load gene that interact genetically with SPAPYUG7.04c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
rescuesalp13MRG family Clr6 histone deacetylase complex subunit Alp13 Phenotypic SuppressionPMID:19547744
External References
Database Identifier Description
NBRP SPAPYUG7.04c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAPYUG7.04c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAPYUG7.04c BioGRID Interaction Datasets
Expression Viewer SPAPYUG7.04c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAPYUG7.04c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAPYUG7.04c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAPYUG7.04c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAPYUG7.04c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAPYUG7.04c Transcriptome Viewer (Bähler Lab)
GEO SPAPYUG7.04c GEO profiles
PInt SPAPYUG7.04c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAPYUG7.04c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAPYUG7.04c Fission yeast phenotypic data & analysis
Cyclebase SPAPYUG7.04c.1 Cell Cycle Data
IntEnz2.7.7.6Integrated relational Enzyme database
Rhea2.7.7.6Annotated reactions database
KEGGMAP03020KEGG Pathway Database
KEGGMAP00230KEGG Pathway Database
KEGGMAP00240KEGG Pathway Database
UniProtKB/SwissProtO74635DNA-directed RNA polymerase II subunit RPB9
ModBaseO74635Database of comparative protein structure models
STRINGO74635Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_594705DNA-directed RNA polymerase II complex subunit Rpb9
RefSeq mRNANM_001020132972h- DNA-directed RNA polymerase II complex subunit Rpb9 (rpb9), mRNA
European Nucleotide ArchiveAB007988ENA EMBL mapping
European Nucleotide ArchiveAF237418ENA EMBL mapping
European Nucleotide ArchiveCU329670ENA EMBL mapping
ePDB3H0GThe European PDB
PDB3H0GPDB
PDBsum3H0GPDBsum
European Nucleotide ArchiveAAL55660ENA Protein Mapping
European Nucleotide ArchiveBAA33021ENA Protein Mapping
European Nucleotide ArchiveCAB66313ENA Protein Mapping
UniParcUPI00001345E7UniProt Archive

Literature for rpb9

Search: Europe PMC or PubMed

Release Version: PomBase:30_57 - 27 Jan 2016