rpb11 (SPAC3A12.07)


Gene Standard Namerpb11 Characterisation Statuspublished
Systematic IDSPAC3A12.07 Feature Typeprotein coding
Synonyms Name Description
ProductRNA polymerase II complex subunit Rpb11 Product Size123aa, 14.13 kDa
Genomic Location Chromosome I, 1433938-1434842 (905nt); CDS:1433953-1434415 (463nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0003677DNA binding385
contributes_toIDAPMID:9322754
GO:0003899DNA-directed RNA polymerase activity37
contributes_toIDAPMID:9322754
GO:0005515protein bindingIPIrpb3PMID:9325316861
IPIrpb2PMID:9325316
GO:0046983protein dimerization activityIEAIPR009025GO_REF:000000252
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006366transcription from RNA polymerase II promoterICGO:0003899GO_REF:0000001137
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005665DNA-directed RNA polymerase II, core complexIDAPMID:932531610
GO:0016591DNA-directed RNA polymerase II, holoenzymeIDAPMID:1052363954
GO:0005829cytosolIDAPMID:168233722316
GO:0005634nucleusIDAPMID:168233722740
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrpb11ΔNullPMID:204732891315
Microscopyrpb11ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopyrpb11ΔNullPECO:0000005, PECO:0000137PMID:23697806624
FYPO:0000314inviable after spore germination with elongated germ tube162
penetrance FYPO_EXT:0000001Microscopyrpb11ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0002262inviable after spore germination, multiple cell divisions, elongated cellMicroscopyrpb11ΔNullPECO:0000005, PECO:0000137PMID:2369780694
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
114339381434002
214340481434137
314341841434842
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
PF01193 Pfam IPR009025 DNA-directed RNA polymerase, RBP11-like dimerisation domain 33 98 3
PS01154 Prosite Patterns IPR008193 DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site 34 65 2
PTHR13946:SF27 HMMPANTHER 1 117 1
PTHR13946 HMMPANTHER 1 117 2
3.30.1360.10 Gene3D 1 112 4
SSF55257 SuperFamily IPR009025 DNA-directed RNA polymerase, RBP11-like dimerisation domain 1 109 4

View domain organization at Pfam

Protein Properties

Ave. residue weight 114.86 Da
Charge -6.00
Isoelectric point 4.66
Molecular weight 14.13 kDa
Number of residues 123
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
29142during GO:0000080PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
30864during GO:0000087PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
24317during GO:0000085PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
4697.04during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
8891.11during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
21756during GO:0072690PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
26440during GO:0000084PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
0.52during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
3during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4569
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3393
conserved in archaea237
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
rpb3RNA polymerase II subunit 3 Dosage RescuePMID:10503538
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
med7mediator complex subunit Med7 Affinity Capture-MSPMID:15182371
rpb3RNA polymerase II subunit 3 Affinity Capture-MSPMID:11839823
Reconstituted ComplexPMID:9548938
Co-purificationPMID:11168400
Affinity Capture-WesternPMID:10503538
Far WesternPMID:9642054
Co-purificationPMID:9325316
Affinity Capture-Western
Reconstituted ComplexPMID:10648788
Co-purification
rpb6DNA-directed RNA polymerase I, II and III subunit Rpb6 Co-purificationPMID:9322754
rpb2RNA polymerase II complex subunit Rpb2 Far WesternPMID:9642054
Co-fractionationPMID:9325316
rpb1RNA polymerase II large subunit Rpb1 Far WesternPMID:9642054
Affinity Capture-WesternPMID:9325316
Reconstituted ComplexPMID:10648788
Affinity Capture-MSPMID:15743411
fcp1CTD phosphatase Fcp1 Affinity Capture-MSPMID:11839823
rpb7DNA-directed RNA polymerase complex II subunit Rpb7 Affinity Capture-MSPMID:16204182
Co-purificationPMID:10523639
External References
Database Identifier Description
NBRP SPAC3A12.07 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC3A12.07 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC3A12.07 BioGRID Interaction Datasets
Expression Viewer SPAC3A12.07 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC3A12.07 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC3A12.07 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC3A12.07 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC3A12.07 Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC3A12.07 Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC3A12.07 Cell Cycle Data
GEO SPAC3A12.07 GEO profiles
PInt SPAC3A12.07 Protein-Protein Interaction Predictor (Bähler Lab)
SPD / RIKEN04/04B11Orfeome Localization Data
KEGGMAP00240KEGG Pathway Database
KEGGMAP03020KEGG Pathway Database
KEGGMAP00230KEGG Pathway Database
WikiGene2543112RNA polymerase II complex subunit Rpb11
EntrezGene2543112RNA polymerase II complex subunit Rpb11
UniProtKB/SwissProtP87123DNA-directed RNA polymerase II subunit RPB11
ModBaseP87123Database of comparative protein structure models
STRINGP87123Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593333RNA polymerase II complex subunit Rpb11
RefSeq mRNANM_001018765972h- RNA polymerase II complex subunit Rpb11 (rpb11), mRNA
European Nucleotide ArchiveAF027822ENA EMBL mapping
European Nucleotide ArchiveD85902ENA EMBL mapping
ePDB3H0GThe European PDB
PDB3H0GPDB
PDBsum3H0GPDBsum
European Nucleotide ArchiveAAB92517ENA Protein Mapping
European Nucleotide ArchiveBAA22801ENA Protein Mapping
European Nucleotide ArchiveBAA22806ENA Protein Mapping
European Nucleotide ArchiveBAA22806.1ENA Protein Mapping
European Nucleotide ArchiveCAB08752ENA Protein Mapping
European Nucleotide ArchiveCAB08752.1ENA Protein Mapping
UniParcUPI00001345EDUniProt Archive

Literature for rpb11

Search: Europe PMC or PubMed

Release Version: PomBase:22_44 - 08 Jul 2014