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 NameCount
DNA binding373
Annotation ExtensionEvidenceWith/FromReference
DNA-directed RNA polymerase activity37
Annotation ExtensionEvidenceWith/FromReference
protein binding862
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
transcription from RNA polymerase II promoter336
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
nucleus2690
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationrpb11Δ1450

Cell Phenotype

Term NameGenotypesCount
abnormal mitotic cell cyclerpb11Δ849
inviable after spore germination with elongated germ tuberpb11Δ164
inviable after spore germination, multiple cell divisions, cell cycle arrest in mitotic interphase, elongated cellsrpb11Δ88
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1433938..1434002, 1434048..1434137, 1434184..1434842
Intron1434003..1434047, 1434138..1434183
5' UTR1433938..1433952AF027822
3' UTR1434416..1434842AF027822
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
PF13656 Pfam 31 101 2
PS01154 Prosite Patterns IPR008193 DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site 34 65 2
PTHR13946 HMMPANTHER 1 123 2
PTHR13946:SF16 HMMPANTHER 1 123 1
3.30.1360.10 Gene3D DNA-directed RNA polymerase, insert domain 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
Codon Adaptation Index 0.48
Isoelectric point 4.66
Molecular weight 14.13 kDa
Number of residues 123
Modifications

Protein Modifications

Term NameResidueCount
ubiquitinylated lysineK61 512
Annotation ExtensionEvidenceResidueReference
IDA PMID:26412298
mass spectrometry evidence K61 PMID:26412298
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
protein levelpresent during GO:0072690Western blot evidencePMID:11918671
decreased during GO:0060274Western blot evidencePMID:11918671

Quantitative Gene Expression

View graphical display of gene expression data for rpb11 (SPAC3A12.07)

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.52during 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


Physical Interactions

Source: BioGRID

Load gene that interact physically with SPAC3A12.07 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
co-purifies withrpb6DNA-directed RNA polymerase I, II and III subunit Rpb6 Co-purificationPMID:9322754
co-purifies withrpb3RNA polymerase II subunit 3 Co-purificationPMID:9325316
co-purifies withrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Co-purificationPMID:10523639
captured byrpb2RNA polymerase II complex subunit Rpb2 Far WesternPMID:9642054
captured byrpb3RNA polymerase II subunit 3 Far WesternPMID:9642054
affinity captured byrpb3RNA polymerase II subunit 3 Affinity Capture-WesternPMID:9325316
affinity captured byred1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
affinity captured byrpb1RNA polymerase II large subunit Rpb1 Affinity Capture-MSPMID:15743411
affinity captured bymed7mediator complex subunit Med7 Affinity Capture-MSPMID:15182371
affinity captured byfcp1CTD phosphatase Fcp1 Affinity Capture-MSPMID:11839823
affinity captured bymtl1TRAMP complex ATP-dependent RNA helicase (predicted) Affinity Capture-MSPMID:24713849
affinity captured byrpb7DNA-directed RNA polymerase complex II subunit Rpb7 Affinity Capture-MSPMID:16204182
co-fractionates withrpb2RNA polymerase II complex subunit Rpb2 Co-fractionationPMID:9325316
capturesrpb1RNA polymerase II large subunit Rpb1 Far WesternPMID:9642054
capturesrpb3RNA polymerase II subunit 3 Far WesternPMID:9642054
capturesrpb2RNA polymerase II complex subunit Rpb2 Far WesternPMID:9642054
forms complex withrpb3RNA polymerase II subunit 3 Reconstituted ComplexPMID:9548938
forms complex withrpb1RNA polymerase II large subunit Rpb1 Reconstituted ComplexPMID:10648788
Genetic Interactions

Source: BioGRID

Load gene that interact genetically with SPAC3A12.07 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
overexpression rescuesrpb3RNA polymerase II subunit 3 Dosage RescuePMID:10503538
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)
GEO SPAC3A12.07 GEO profiles
PInt SPAC3A12.07 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC3A12.07 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC3A12.07 Fission yeast phenotypic data & analysis
Cyclebase SPAC3A12.07.1 Cell Cycle Data
KEGGMAP00240KEGG Pathway Database
KEGGMAP00230KEGG Pathway Database
KEGGMAP03020KEGG Pathway Database
SPD / RIKEN04/04B11Orfeome Localization Data
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 ArchiveCU329670ENA EMBL mapping
European Nucleotide ArchiveD85902ENA EMBL mapping
European Nucleotide ArchiveD89597ENA EMBL mapping
ePDB3H0GThe European PDB
PDB3H0GPDB
PDBsum3H0GPDBsum
European Nucleotide ArchiveAAB92517ENA Protein Mapping
European Nucleotide ArchiveBAA22801ENA Protein Mapping
European Nucleotide ArchiveBAA22806ENA Protein Mapping
European Nucleotide ArchiveCAB08752ENA Protein Mapping
KEGG00230+2.7.7.6Purine metabolism
KEGG00240+2.7.7.6Pyrimidine metabolism
UniParcUPI00001345EDUniProt Archive

Literature for rpb11

Search: Europe PMC or PubMed

Release Version: PomBase:30_57 - 27 Jan 2016