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 binding379
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase activity37
Annotation ExtensionEvidenceWith/FromReference
zinc ion binding248
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
transcription from RNA polymerase II promoter334
Annotation ExtensionEvidenceWith/FromReference
transcription-coupled nucleotide-excision repair7
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2316
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase II, core complex11
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase II, holoenzyme56
Annotation ExtensionEvidenceWith/FromReference
nucleus2697
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
normal growth on sodium butyraterpb9ΔNull55
normal growth on trichostatin Arpb9ΔNull113
sensitive to 5-fluorouracilrpb9ΔNull271
sensitive to valproic acidrpb9ΔNull155
viable vegetative cell populationrpb9ΔNull3783

Cell Phenotype

Term NameAlleleExpressionCount
viable vegetative cell with normal cell morphologyrpb9ΔNull3092
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
exon4752332..4752292,4752224..4752158,4752034..4751985,4751942..4751810,4751734..4751684
mRNA4752521..4751390
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
PF01096 Pfam IPR001222 Zinc finger, TFIIS-type 74 110 4
PF02150 Pfam IPR001529 DNA-directed RNA polymerase, M/15kDa subunit 4 36 3
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:SF1 HMMPANTHER 1 113 1
PTHR11239 HMMPANTHER 1 113 3
2.20.25.10 Gene3D 51 112 7
2.20.25.10 Gene3D 1 46 7
SSF57783 SuperFamily 1 48 8
SSF57783 SuperFamily 54 112 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 fungi4604
conserved in eukaryotes4516
conserved in metazoa3432
conserved in vertebrates3407
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
affinity captured byfcp1CTD phosphatase Fcp1 Affinity Capture-MSPMID:11839823
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
co-purifies withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-purificationPMID:10523639
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withacp2F-actin capping protein beta subunit Acp2 Negative GeneticPMID:22681890
negative genetic interaction withada1adenosine deaminase Ada1 Negative GeneticPMID:22681890
negative genetic interaction withadn2transcription factor (predicted) Negative GeneticPMID:22681890
positive genetic interaction withago1argonaute Positive GeneticPMID:18818364
positive genetic interaction withago1argonaute Positive GeneticPMID:22681890
negative genetic interaction withair1zinc knuckle TRAMP complex subunit Air1 Negative GeneticPMID:18818364
negative genetic interaction witharv1Arv1-like family protein Arv1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withase1antiparallel microtubule cross-linking factor Ase1 Negative GeneticPMID:22681890
negative genetic interaction withase1antiparallel microtubule cross-linking factor Ase1 Negative GeneticPMID:22681890
negative genetic interaction withash2Ash2-trithorax family protein Negative GeneticPMID:18818364
negative genetic interaction withash2Ash2-trithorax family protein Negative GeneticPMID:22681890
negative genetic interaction withash2Ash2-trithorax family protein Negative GeneticPMID:22681890
negative genetic interaction withbdf2BET family double bromodomain protein Bdf2 Negative GeneticPMID:18818364
negative genetic interaction withbdf2BET family double bromodomain protein Bdf2 Negative GeneticPMID:22681890
negative genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withcdk11serine/threonine protein kinase cdk11 Positive GeneticPMID:18818364
positive genetic interaction withcdt2WD repeat protein Cdt2 Positive GeneticPMID:22681890
negative genetic interaction withcho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Negative GeneticPMID:18818364
positive genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:18818364
positive genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:22681890
positive genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:22681890
negative genetic interaction withclr5Clr5 protein Negative GeneticPMID:22681890
negative genetic interaction withcpd1tRNA (m1A) methyltransferase complex catalytic subunit Cpd1 Negative GeneticPMID:18818364
positive genetic interaction withcsn5COP9/signalosome complex subunit Csn5 Positive GeneticPMID:22681890
positive genetic interaction withcsn5COP9/signalosome complex subunit Csn5 Positive GeneticPMID:22681890
negative genetic interaction withcwf16splicing factor Cwf16 Negative GeneticPMID:22681890
positive genetic interaction withdcr1dicer Positive GeneticPMID:18818364
positive genetic interaction withdcr1dicer Positive GeneticPMID:22681890
negative genetic interaction withdeg1tRNA-pseudouridine synthase Deg1 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withdep1Sds3-like family protein Dep1 Negative GeneticPMID:22681890
negative genetic interaction witheca39branched chain amino acid aminotransferase Eca39 Negative GeneticPMID:22681890
negative genetic interaction withelp1elongator subunit Elp1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withgcd10tRNA (m1A) methyltransferase Gcd10 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withgmh6alpha-1,2-galactosyltransferase Gmh6 Negative GeneticPMID:22681890
negative genetic interaction withgyp1GTPase activating protein Gyp1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withhip4histone promoter control protein Hip4 Positive GeneticPMID:22681890
positive genetic interaction withhrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Positive GeneticPMID:18818364
positive genetic interaction withhrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Positive GeneticPMID:22681890
negative genetic interaction withidp1isocitrate dehydrogenase Idp1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withimp1importin alpha Negative GeneticPMID:22681890
negative genetic interaction withlsc1Lsk1 associated cyclin Negative GeneticPMID:22681890
negative genetic interaction withlsk1P-TEFb-associated cyclin-dependent protein kinase Lsk1 Negative GeneticPMID:18818364
positive genetic interaction withlub1WD repeat protein Lub1 Positive GeneticPMID:22681890
positive genetic interaction withlub1WD repeat protein Lub1 Positive GeneticPMID:22681890
positive genetic interaction withmad1mitotic spindle checkpoint protein Mad1 Positive GeneticPMID:18818364
negative genetic interaction withmed20mediator complex subunit Med20 Negative GeneticPMID:18818364
negative genetic interaction withmed6mediator complex subunit Med6 Negative GeneticPMID:18818364
negative genetic interaction withmfr1fizzy-related protein Mfr1 Negative GeneticPMID:22681890
positive genetic interaction withmsh1mitochondrial MutS protein Msh1 (predicted) Positive GeneticPMID:18818364
negative genetic interaction withmtg1mitochondrial GTPase involved in translation Mtg1 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withpam17TIM23 translocase complex-associated motor subunit Pam17 (predicted) Positive GeneticPMID:22681890
negative genetic interaction withpef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:22681890
negative genetic interaction withpht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:18818364
negative genetic interaction withpht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:22681890
negative genetic interaction withpht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:22681890
negative genetic interaction withpnk1DNA kinase/phosphatase Pnk1 Negative GeneticPMID:22681890
negative genetic interaction withpnk1DNA kinase/phosphatase Pnk1 Negative GeneticPMID:22681890
negative genetic interaction withppa2serine/threonine protein phosphatase Ppa2 Negative GeneticPMID:22681890
negative genetic interaction withpsh3ER chaperone SHR3 homologue Psh3 Negative GeneticPMID:22681890
negative genetic interaction withptc2protein phosphatase 2C Ptc2 Negative GeneticPMID:18818364
positive genetic interaction withrad55RecA family ATPase Rad55/Rhp55 Positive GeneticPMID:22681890
positive genetic interaction withrad55RecA family ATPase Rad55/Rhp55 Positive GeneticPMID:22681890
positive genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:18818364
positive genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:22681890
positive genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Positive GeneticPMID:22681890
positive genetic interaction withraf2Rik1-associated factor Raf2 Positive GeneticPMID:18818364
positive genetic interaction withraf2Rik1-associated factor Raf2 Positive GeneticPMID:22681890
positive genetic interaction withraf2Rik1-associated factor Raf2 Positive GeneticPMID:22681890
negative genetic interaction withrbd1mitochondrial rhomboid protease (predicted) Negative GeneticPMID:22681890
negative genetic interaction withreb1RNA polymerase I transcription termination factor/ RNA polymerase II transcription factor Reb1 Negative GeneticPMID:18818364
negative genetic interaction withrhn1RNA polymerase II transcription termination factor homolog Negative GeneticPMID:22681890
negative genetic interaction withrhn1RNA polymerase II transcription termination factor homolog Negative GeneticPMID:22681890
positive genetic interaction withrik1silencing protein Rik1 Positive GeneticPMID:18818364
positive genetic interaction withrik1silencing protein Rik1 Positive GeneticPMID:22681890
positive genetic interaction withrik1silencing protein Rik1 Positive GeneticPMID:22681890
positive genetic interaction withrpl160160S ribosomal protein L13/L16 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withrpl160160S ribosomal protein L13/L16 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withryh1GTPase Ryh1 Positive GeneticPMID:18818364
negative genetic interaction withsap114U2 snRNP subunit Sap114 Negative GeneticPMID:22681890
negative genetic interaction withsdc1Dpy-30 domain protein Sdc1 Negative GeneticPMID:18818364
negative genetic interaction withsdc1Dpy-30 domain protein Sdc1 Negative GeneticPMID:22681890
negative genetic interaction withsec28coatomer epsilon subunit (predicted) Negative GeneticPMID:18818364
negative genetic interaction withsnf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:18818364
negative genetic interaction withsnf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:22681890
negative genetic interaction withsnf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:22681890
negative genetic interaction withsnt2Lid2 complex subunit Snt2 Negative GeneticPMID:18818364
negative genetic interaction withsnt2Lid2 complex subunit Snt2 Negative GeneticPMID:22681890
negative genetic interaction withsnt2Lid2 complex subunit Snt2 Negative GeneticPMID:22681890
negative genetic interaction withsnz1pyridoxine biosynthesis protein Negative GeneticPMID:22681890
negative genetic interaction withsol1SWI/SNF complex subunit Sol1 Negative GeneticPMID:22681890
synthetic growth defect withSPBC1347.08cribonuclease H2 complex subunit (predicted) Synthetic Growth DefectPMID:18931302
negative genetic interaction withSPBC16H5.12cconserved fungal protein Negative GeneticPMID:22681890
negative genetic interaction withSPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
negative genetic interaction withSPBC36B7.08cnucleosome assembly protein (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC36B7.08cnucleosome assembly protein (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC4B4.04translation initiation factor eIF2A (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC4B4.04translation initiation factor eIF2A (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC577.11DUF3074 family protein Negative GeneticPMID:22681890
negative genetic interaction withSPBC725.01aspartate aminotransferase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC9B6.03zf-FYVE type zinc finger protein Negative GeneticPMID:22681890
negative genetic interaction withSPBPB2B2.18Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withSPCC16C4.106-phosphogluconolactonase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPCC16C4.106-phosphogluconolactonase (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPCC18.10pyridoxine-pyridoxal-pyridoxamine kinase (predicted) Negative GeneticPMID:18818364
negative genetic interaction withSPCC18.13tRNA (guanine-N7-)-methyltransferase subunit Trm82 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withSPCC18.13tRNA (guanine-N7-)-methyltransferase subunit Trm82 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPCC18.13tRNA (guanine-N7-)-methyltransferase subunit Trm82 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPCC1840.09NAD dependent epimerase/dehydratase family protein Negative GeneticPMID:22681890
negative genetic interaction withSPCC1919.13cribosome biogenesis protein (predicted) Negative GeneticPMID:18818364
negative genetic interaction withspn3mitotic septin Spn3 Negative GeneticPMID:22681890
positive genetic interaction withsrb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
positive genetic interaction withsrb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
negative genetic interaction withssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withtas3RITS complex subunit 3 Positive GeneticPMID:18818364
positive genetic interaction withtas3RITS complex subunit 3 Positive GeneticPMID:22681890
negative genetic interaction withtif38translation initiation factor eIF3h (p40) Negative GeneticPMID:22681890
negative genetic interaction withtrm112protein and tRNA methyltransferase regulatory subunit Trm112 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withtrm8tRNA (guanine-N7-)-methyltransferase catalytic subunit Trm8 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withtsc1hamartin Negative GeneticPMID:22681890
negative genetic interaction withtsc1hamartin Negative GeneticPMID:22681890
negative genetic interaction withuap2U2 snRNP-associated protein Uap2 Negative GeneticPMID:22681890
positive genetic interaction withura5orotate phosphoribosyltransferase Ura5 Positive GeneticPMID:22681890
positive genetic interaction withura5orotate phosphoribosyltransferase Ura5 Positive GeneticPMID:22681890
negative genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:18818364
negative genetic interaction withvps901guanyl-nucleotide exchange factor Vps901 (predicted) Negative GeneticPMID:22681890
positive genetic interaction withvsl1vacuolar SNARE Vsl1/Vam7 Positive GeneticPMID:22681890
negative genetic interaction withxap5xap-5-like protein Negative GeneticPMID:24957674
negative genetic interaction withzrg17cation diffusion family zinc transmembrane transporter Zrg17 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:25_49 - 02 Feb 2015