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 binding383
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase activity37
Annotation ExtensionEvidenceWith/FromReference
zinc ion binding249
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
transcription from RNA polymerase II promoter335
Annotation ExtensionEvidenceWith/FromReference
transcription-coupled nucleotide-excision repair7
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2315
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase II, core complex11
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase II, holoenzyme55
Annotation ExtensionEvidenceWith/FromReference
nucleus2740
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002619normal growth on sodium butyrateCell growth assayrpb9ΔNullPECO:0000005, PECO:0000201, PECO:0000142PMID:2386193755
FYPO:0002620normal growth on trichostatin ACell growth assayrpb9ΔNullPECO:0000005, PECO:0000201, PECO:0000142PMID:23861937110
FYPO:0000115sensitive to valproic acid155
expressivity FYPO_EXT:0000003Cell growth assayrpb9ΔNullPECO:0000201, PECO:0000005, PECO:0000142PMID:23861937
FYPO:0002060viable vegetative cell populationMicroscopyrpb9ΔNullPMID:204732893759
Microscopyrpb9ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphology3089
penetrance FYPO_EXT:0000001Microscopyrpb9ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
147525214752292
247522244752158
347520344751985
447519424751810
547517344751390

UTRs

Region Coordinates Reference
five_prime_UTR4752521..4752333PMID:21511999
three_prime_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
PS01030 Prosite Patterns IPR019761 DNA-directed RNA polymerase M, 15kDa subunit, conserved site 6 32 3
PS00466 Prosite Patterns IPR001222 Zinc finger, TFIIS-type 75 110 3
PS51133 Prosite Profiles IPR001222 Zinc finger, TFIIS-type 71 111 4
PTHR11239 HMMPANTHER 1 112 3
2.20.25.10 Gene3D 51 112 7
2.20.25.10 Gene3D 1 46 7
SSF57783 SuperFamily 54 112 8
SSF57783 SuperFamily 1 48 8
PIRSF005586 PIRSF IPR012164 DNA-directed RNA polymerase, subunit C11/M/9 1 113 3

View domain organization at Pfam

Protein Properties

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

Quantitative Gene Expression

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
5.2during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
1.2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
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

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
fcp1CTD phosphatase Fcp1 Affinity Capture-MSPMID:11839823
rpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-purificationPMID:10523639
rpb1RNA polymerase II large subunit Rpb1 Affinity Capture-MSPMID:15743411
rpb3RNA polymerase II subunit 3 Affinity Capture-MSPMID:11839823
Reconstituted ComplexPMID:10648788
Co-purificationPMID:11168400
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
med20mediator complex subunit Med20 Negative GeneticPMID:18818364
pnk1DNA kinase/phosphatase Pnk1 Negative GeneticPMID:22681890
rik1silencing protein Rik1 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
ada1adenosine deaminase Ada1 Negative GeneticPMID:22681890
pef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:22681890
SPCC16C4.106-phosphogluconolactonase (predicted) Negative GeneticPMID:22681890
SPAC821.05translation initiation factor eIF3h (p40) Negative GeneticPMID:22681890
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:18818364
uap2U2 snRNP-associated protein Uap2 Negative GeneticPMID:22681890
snf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
gyp1GTPase activating protein Gyp1 (predicted) Negative GeneticPMID:22681890
ash2Ash2-trithorax family protein Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
SPBC577.11DUF3074 family protein Negative GeneticPMID:22681890
SPCC1840.09NAD dependent epimerase/dehydratase family protein Negative GeneticPMID:22681890
med6mediator complex subunit Med6 Negative GeneticPMID:18818364
ccr4CCR4-Not complex subunit Ccr4 (predicted) Negative GeneticPMID:22681890
tas3RITS complex subunit 3 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
hip4histone promoter control protein Hip4 Positive GeneticPMID:22681890
gmh6alpha-1,2-galactosyltransferase Gmh6 Negative GeneticPMID:22681890
idp1isocitrate dehydrogenase Idp1 (predicted) Negative GeneticPMID:22681890
dep1Sds3-like family protein Dep1 Negative GeneticPMID:22681890
mfr1fizzy-related protein Mfr1 Negative GeneticPMID:22681890
SPBC4B4.04translation initiation factor eIF2A (predicted) Negative GeneticPMID:22681890
lsc1Lsk1 associated cyclin Negative GeneticPMID:22681890
ryh1GTPase Ryh1 Positive GeneticPMID:18818364
gcd10tRNA (m1A) methyltransferase Gcd10 (predicted) Negative GeneticPMID:22681890
lub1WD repeat protein Lub1 Positive GeneticPMID:22681890
ago1argonaute Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
SPBC1347.08cribonuclease H2 complex subunit (predicted) Synthetic Growth DefectPMID:18931302
SPCC594.06cvacuolar SNARE Vam7 (predicted) Positive GeneticPMID:22681890
raf2Rik1-associated factor Raf2 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
elp1elongator subunit Elp1 (predicted) Negative GeneticPMID:22681890
cdk11serine/threonine protein kinase cdk11 Positive GeneticPMID:18818364
imp1importin alpha Negative GeneticPMID:22681890
bdf2BET family double bromodomain protein Bdf2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
srb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
pht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
arv1Arv1-like family protein Arv1 (predicted) Negative GeneticPMID:22681890
tsc1hamartin Negative GeneticPMID:22681890
air1zinc knuckle TRAMP complex subunit Air1 Negative GeneticPMID:18818364
deg1tRNA-pseudouridine synthase (predicted) Negative GeneticPMID:18818364
SPBPB2B2.18Schizosaccharomyces specific protein Negative GeneticPMID:22681890
vps901guanyl-nucleotide exchange factor Vps901 (predicted) Negative GeneticPMID:22681890
ppa2serine/threonine protein phosphatase Ppa2 Negative GeneticPMID:22681890
spn3septin Spn3 Negative GeneticPMID:22681890
clr5Clr5 protein Negative GeneticPMID:22681890
ase1antiparallel microtubule cross-linking factor Ase1 Negative GeneticPMID:22681890
rbd1mitochondrial rhomboid protease (predicted) Negative GeneticPMID:22681890
trm8tRNA (guanine-N7-)-methyltransferase catalytic subunit Trm8 (predicted) Negative GeneticPMID:22681890
snz1pyridoxine biosynthesis protein Negative GeneticPMID:22681890
clr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
cwf16splicing factor Cwf16 Negative GeneticPMID:22681890
cho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Negative GeneticPMID:18818364
acp2F-actin capping protein beta subunit Acp2 Negative GeneticPMID:22681890
rad55RecA family ATPase Rad55/Rhp55 Positive GeneticPMID:22681890
pam17TIM23 translocase complex-associated motor subunit Pam17 (predicted) Positive GeneticPMID:22681890
sol1SWI/SNF complex subunit Sol1 Negative GeneticPMID:22681890
mtg1mitochondrial GTPase involved in translation Mtg1 (predicted) Negative GeneticPMID:22681890
msh1mitochondrial MutS protein Msh1 (predicted) Positive GeneticPMID:18818364
csn5COP9/signalosome complex subunit Csn5 Positive GeneticPMID:22681890
snt2Lid2 complex subunit Snt2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
rpl160160S ribosomal protein L13/L16 (predicted) Positive GeneticPMID:22681890
hrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
ptc2protein phosphatase 2C Ptc2 Negative GeneticPMID:18818364
sec28coatomer epsilon subunit (predicted) Negative GeneticPMID:18818364
rhn1RNA polymerase II transcription termination factor homolog Negative GeneticPMID:22681890
reb1RNA polymerase I transcription termination factor/ RNA polymerase II transcription factor Reb1 Negative GeneticPMID:18818364
raf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
sap114U2 snRNP subunit Sap114 Negative GeneticPMID:22681890
cpd1tRNA (m1A) methyltransferase complex catalytic subunit Cpd1 Negative GeneticPMID:18818364
cdt2WD repeat protein Cdt2 Positive GeneticPMID:22681890
eca39branched chain amino acid aminotransferase Eca39 Negative GeneticPMID:22681890
SPBC9B6.03zf-FYVE type zinc finger protein Negative GeneticPMID:22681890
mad1mitotic spindle checkpoint protein Mad1 Positive GeneticPMID:18818364
lsk1P-TEFb-associated cyclin-dependent protein kinase Lsk1 Negative GeneticPMID:18818364
xap5xap-5-like protein Negative GeneticPMID:24957674
adn2transcription factor (predicted) Negative GeneticPMID:22681890
SPBC16H5.12cconserved fungal protein Negative GeneticPMID:22681890
SPBC725.01aspartate aminotransferase (predicted) Negative GeneticPMID:22681890
SPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
trm112protein and tRNA methyltransferase regulatory subunit Trm112 (predicted) Negative GeneticPMID:22681890
sdc1Dpy-30 domain protein Sdc1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
SPCC1919.13cribosome biogenesis protein (predicted) Negative GeneticPMID:18818364
SPCC18.10pyridoxine-pyridoxal-pyridoxamine kinase (predicted) Negative GeneticPMID:18818364
psh3ER chaperone SHR3 homologue Psh3 Negative GeneticPMID:22681890
SPCC18.13tRNA (guanine-N7-)-methyltransferase subunit Trm82 (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
ura5orotate phosphoribosyltransferase Ura5 Positive GeneticPMID:22681890
ssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
zrg17cation diffusion family zinc membrane transporter Zrg17 Negative GeneticPMID:22681890
dcr1dicer Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
SPBC36B7.08cnucleosome assembly protein (predicted) Negative GeneticPMID:22681890
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)
Cyclebase SPAPYUG7.04c Cell Cycle Data
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
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
ePDB3H0GThe European PDB
PDB3H0GPDB
PDBsum3H0GPDBsum
European Nucleotide ArchiveAAL55660.1ENA Protein Mapping
European Nucleotide ArchiveBAA33021.1ENA Protein Mapping
European Nucleotide ArchiveCAB66313.1ENA Protein Mapping
UniParcUPI00001345E7UniProt Archive

Literature for rpb9

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014