rpb9 (SPAPYUG7.04c)

Gene Standard Namerpb9 ChromosomeI
Systematic IDSPAPYUG7.04c Gene Start4752521
Synonyms Gene End4751390
ProductDNA-directed RNA polymerase II complex subunit Rpb9 Gene Length1132
Feature Typeprotein coding CDS Start4752332
Name Description CDS End4751684
Characterisation Statuspublished CDS Length649

Ensembl Gene Location
  1. tfa1
  2. sin1
  3. SPNCRNA.1021
  4. mid2
  5. rpb9
  6. SPAPYUG7.05
  7. SPNCRNA.1022
  8. mug67
  9. ecm29
Fission Yeast Phenotype Ontology

Ontology Graph

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Term IDTerm NameEvidenceAlleleAllele TypeExpressionConditionReference
FYPO:0002060viable vegetative cell populationMicroscopyrpb9delta (deletion)deletionPMID:20473289
GO Molecular Function

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Term IDTerm NameEvidenceWith/FromReference
GO:0003677DNA bindingIEAIPR001529GO_REF:0000002
GO:0003899DNA-directed RNA polymerase activity
contributes_toIDAPMID:9852944
GO:0008270zinc ion bindingIEAIPR001222, IPR012164GO_REF:0000002
GO Biological Process

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Term IDTerm NameEvidenceWith/FromReference
GO:0006283transcription-coupled nucleotide-excision repairISOSGD:S000003038GO_REF:0000024
GO:0006366transcription from RNA polymerase II promoterICGO:0016591PMID:9852944
GO Cellular Component

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Term IDTerm NameEvidenceWith/FromReference
GO:0005634nucleusIDAPMID:16823372
GO:0005829cytosolIDAPMID:16823372
GO:0016591DNA-directed RNA polymerase II, holoenzymeTASPMID:9852944
Transcript
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Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
147525214752292
247522244752158
347520344751985
447519424751810
547517344751390

References

Region Start End Reference
three_prime_UTR47516834751390PMID:21511999
five_prime_UTR47525214752333PMID:21511999
three_prime_UTR47516834751390PMID:21511999
Protein Features
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Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID InterPro Database Description Start End All Genes
PF02150 IPR001529 Pfam DNA-directed RNA polymerase, M/15kDa subunit 4 36 3
PF01096 IPR001222 Pfam Zinc finger, TFIIS-type 74 110 4
SM00661 IPR001529 SMART DNA-directed RNA polymerase, M/15kDa subunit 5 58 3
SM00440 IPR001222 SMART Zinc finger, TFIIS-type 73 112 4
PS51133 IPR001222 Prosite Profiles Zinc finger, TFIIS-type 71 111 4
PS01030 IPR019761 Prosite Patterns DNA-directed RNA polymerase M, 15kDa subunit, conserved site 6 32 3
PS00466 IPR001222 Prosite Patterns Zinc finger, TFIIS-type 75 110 3
G3DSA:2.20.25.10 Gene3D 1 46 7
G3DSA:2.20.25.10 Gene3D 51 112 7
SSF57783 SuperFamily 1 48 8
SSF57783 SuperFamily 54 112 8
PIRSF005586 IPR012164 PIRSF DNA-directed RNA polymerase, subunit C11/M/9 1 113 3
PTHR11239 hmmpanther 1 113 3
PTHR11239:SF1 hmmpanther 1 113 1

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
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Gene Expression
DescriptionEvidenceDuringConditionRangeAverage per CellReference
protein levelexperimental evidencesingle-celled organism vegetative growth phasePECO:0000014,
PECO:0000005		population_wide7147.16PMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide3957.79PMID:23101633
RNA levelexperimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide1.2PMID:23101633
experimental evidencesingle-celled organism vegetative growth phasePECO:0000014,
PECO:0000005		population_wide5.2PMID:23101633
Species Distribution
DescriptionQualifierReference
predominantly single copy (one to one)
conserved in fungi
conserved in eukaryotes
conserved in metazoa
conserved in vertebrates
conserved in archaea
Manually curated orthologous groups
SpeciesGeneDescription

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Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
ptc2protein phosphatase 2C Ptc2 Negative GeneticPMID:18818364
rhn1RNA polymerase II transcription termination factor homolog Negative GeneticPMID:22681890
snz1pyridoxine biosynthesis protein Negative GeneticPMID:22681890
SPCC18.13tRNA (guanine-N7-)-methyltransferase subunit Trm82 (predicted) Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
sdc1Dpy-30 domain protein Sdc1 Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
acp2F-actin capping protein beta subunit (predicted) Negative GeneticPMID:22681890
sol1SWI/SNF complex subunit Sol1 Negative GeneticPMID:22681890
clr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
pmc5mediator complex subunit Pmc5 Negative GeneticPMID:18818364
ash2Ash2-trithorax family protein Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
psh3ER chaperone SHR3 homologue Psh3 Negative GeneticPMID:22681890
SPCC1919.13cribosome biogenesis protein (predicted) Negative GeneticPMID:18818364
spn3septin Spn3 Negative GeneticPMID:22681890
trm8tRNA (guanine-N7-)-methyltransferase catalytic subunit Trm8 (predicted) Negative GeneticPMID:22681890
tsc1hamartin Negative GeneticPMID:22681890
ago1argonaute Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
SPBC1289.13calpha-1,2-galactosyltransferase (predicted) Negative GeneticPMID:22681890
idp1isocitrate dehydrogenase Idp1 (predicted) Negative GeneticPMID:22681890
ase1antiparallel microtubule cross-linking factor Ase1 Negative GeneticPMID:22681890
vps901guanyl-nucleotide exchange factor Vps901 (predicted) Negative GeneticPMID:22681890
SPBPB2B2.18sequence orphan Negative GeneticPMID:22681890
dep1Sds3-like family protein Dep1 Negative GeneticPMID:22681890
eca39branched chain amino acid aminotransferase Eca39 Negative GeneticPMID:22681890
snf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
rad55RecA family ATPase Rad55/Rhp55 Positive GeneticPMID:22681890
pnk1DNA kinase/phosphatase Pnk1 Negative GeneticPMID:22681890
reb1RNA polymerase I transcription termination factor Reb1 Negative GeneticPMID:18818364
lub1WD repeat protein Lub1 Positive GeneticPMID:22681890
zrg17cation diffusion family zinc membrane transporter Zrg17 Negative GeneticPMID:22681890
SPCC18.10pyridoxine-pyridoxal-pyridoxamine kinase (predicted) Negative GeneticPMID:18818364
SPAC25B8.05tRNA-pseudouridine synthase (predicted) Negative GeneticPMID:18818364
sap114U2 snRNP subunit Sap114 Negative GeneticPMID:22681890
uap2U2 snRNP-associated protein Uap2 Negative GeneticPMID:22681890
SPCC1840.09NAD dependent epimerase/dehydratase family protein Negative GeneticPMID:22681890
gcd10tRNA (m1A) methyltransferase, translation initiation factor eIF-3 gamma subunit Gcd10 (predicted) Negative GeneticPMID:22681890
msh1mitochondrial MutS protein Msh1 (predicted) Positive GeneticPMID:18818364
SPAC821.05translation initiation factor eIF3h (p40) Negative GeneticPMID:22681890
SPBC36B7.08cnucleosome assembly protein (predicted) Negative GeneticPMID:22681890
srb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
imp1importin alpha Negative GeneticPMID:22681890
pef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:22681890
arv1Arv1-like family protein Arv1 (predicted) Negative GeneticPMID:22681890
clr5Clr5 protein Negative GeneticPMID:22681890
SPCC594.06cvacuolar SNARE Vam7 (predicted) Positive GeneticPMID:22681890
adn2transcription factor (predicted) Negative GeneticPMID:22681890
tas3RITS complex subunit 3 Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
gyp1GTPase activating protein Gyp1 (predicted) Negative GeneticPMID:22681890
raf2Rik1-associated factor Raf2 Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
air1zinc knuckle TRAMP complex subunit Air1 Negative GeneticPMID:18818364
pam17TIM23 translocase complex-associated motor subunit Pam17 (predicted) Positive GeneticPMID:22681890
trm112protein and tRNA methyltransferase regulatory subunit Trm112 (predicted) Negative GeneticPMID:22681890
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:18818364
lsc1Lsk1 associated cyclin Negative GeneticPMID:22681890
mtg1mitochondrial GTPase involved in translation Mtg1 (predicted) Negative GeneticPMID:22681890
rpl160160S ribosomal protein L13/L16 (predicted) Positive GeneticPMID:22681890
SPBC577.11DUF3074 family protein Negative GeneticPMID:22681890
med20mediator complex subunit Med20 Negative GeneticPMID:18818364
hrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
cwf16splicing factor Cwf16 Negative GeneticPMID:22681890
ccr4CCR4-Not complex subunit Ccr4 (predicted) Negative GeneticPMID:22681890
elp1elongator subunit Elp1 (predicted) Negative GeneticPMID:22681890
SPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
SPBC725.01aspartate aminotransferase (predicted) Negative GeneticPMID:22681890
raf1Rik1-associated factor Raf1 Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
SPBC16H5.12cconserved fungal protein Negative GeneticPMID:22681890
SPBC9B6.03zf-FYVE type zinc finger protein Negative GeneticPMID:22681890
ura5orotate phosphoribosyltransferase Ura5 Positive GeneticPMID:22681890
snt2Lid2 complex subunit Snt2 Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
cdt2WD repeat protein Cdt2 Positive GeneticPMID:22681890
SPBC4B4.04translation initiation factor eIF2A (predicted) Negative GeneticPMID:22681890
nrc1bromodomain protein (predicted) Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
SPBC1347.08cribonuclease H2 complex subunit (predicted) Synthetic Growth DefectPMID:18931302
sec28coatomer epsilon subunit (predicted) Negative GeneticPMID:18818364
ryh1GTPase Ryh1 Positive GeneticPMID:18818364
lsk1P-TEFb-associated cyclin-dependent protein kinase Lsk1 Negative GeneticPMID:18818364
csn5COP9/signalosome complex subunit Csn5 Positive GeneticPMID:22681890
ppa2serine/threonine protein phosphatase Ppa2 Negative GeneticPMID:22681890
pht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
cdk11serine/threonine protein kinase cdk11 Positive GeneticPMID:18818364
SPBC13E7.11mitochondrial rhomboid protease (predicted) Negative GeneticPMID:22681890
SPCC16C4.106-phosphogluconolactonase (predicted) Negative GeneticPMID:22681890
cho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Negative GeneticPMID:18818364
rik1silencing protein Rik1 Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
dcr1dicer Positive GeneticPMID:22681890
Positive GeneticPMID:18818364
mad1mitotic spindle checkpoint protein Mad1 Positive GeneticPMID:18818364
cpd1tRNA (m1A) methyltransferase complex catalytic subunit Cpd1 Negative GeneticPMID:18818364
mfr1fizzy-related protein Mfr1 Negative GeneticPMID:22681890
ada1adenosine deaminase Ada1 (predicted) Negative GeneticPMID:22681890
ssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
hip4histone promoter control protein Hip4 Positive GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
rpb3RNA polymerase II subunit 3 Affinity Capture-MSPMID:11839823
Co-purificationPMID:11168400
Reconstituted ComplexPMID:10648788
rpb1RNA polymerase II large subunit Rpb1 Affinity Capture-MSPMID:15743411
rpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-purificationPMID:10523639
fcp1CTD phosphatase Fcp1 Affinity Capture-MSPMID:11839823
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External References
Database Identifier Description
NBRP SPAPYUG7.04c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAPYUG7.04c Retrieval of eukaryotic orthologs
BioGrid SPAPYUG7.04c BioGRID Interaction Datasets
Bähler Lab SPAPYUG7.04c Cell Cycle Expression Profile
Bähler Lab SPAPYUG7.04c Meiosis/Sporulation Expression Profies
Bähler Lab SPAPYUG7.04c Pheromone response/mating expression profiles
Bähler Lab SPAPYUG7.04c Environmental stress expression profiles
Bähler Lab SPAPYUG7.04c Bähler Lab Transcriptome Viewer
Cyclebase SPAPYUG7.04c Cell Cycle Data
PInt SPAPYUG7.04c Bähler Lab Protein-Protein Interaction Predictor
Entrez Gene SPAPYUG7.04c Entrez Gene
WikiGene2541470DNA-directed RNA polymerase II complex subunit Rpb9
Uniprot_genenameRPB9
EntrezGene2541470DNA-directed RNA polymerase II complex subunit Rpb9
KEGGMAP00240
IntEnz2.7.7.6
KEGGMAP03020
KEGGMAP00230
UniProtKB/SwissProtO74635DNA-directed RNA polymerase II subunit RPB9
ModBaseO74635Database of comparative protein structure models
Pfam Protein DomainsO74635Pfam Domain Arrangement
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 ArchiveAAL55660ENA Protein Mapping
European Nucleotide ArchiveBAA33021ENA Protein Mapping
European Nucleotide ArchiveCAB66313ENA Protein Mapping
UniParcUPI00001345E7UniProt Archive

Literature for rpb9
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Search: UK PMC or PubMed

Release Version: PomBase:18_35 - 11 May 2013