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General Information
Symbol
Dmel\Polr2I
Species
D. melanogaster
Name
RNA polymerase II subunit I
Annotation Symbol
CG3284
Feature Type
FlyBase ID
FBgn0004855
Gene Model Status
Stock Availability
Gene Summary
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template (By similarity). (UniProt, P36958)
Contribute a Gene Snapshot for this gene.
Also Known As

RNA polymerase II, RpII15, PolII, Pol II, RNAP II

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-55
RefSeq locus
NT_033777 REGION:14309089..14310178
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000133051
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001222
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR001222, InterPro:IPR012164
(assigned by InterPro )
Biological Process (6 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in mitotic cell cycle
inferred from high throughput mutant phenotype
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in mRNA cleavage
inferred from electronic annotation with InterPro:IPR034012
(assigned by InterPro )
inferred from sequence or structural similarity with UniProtKB:P36954
inferred from biological aspect of ancestor with PANTHER:PTN000133107
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000133107
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000133107
(assigned by GO_Central )
inferred from sequence or structural similarity with UniProtKB:P36954
Protein Family (UniProt)
Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family. (P36958)
Summaries
Gene Group (FlyBase)
RNA POLYMERASE II -
RNA Polymerase II (RNAP II) synthesizes mRNAs and a variety of non-coding RNAs, including snRNAs, snoRNAs, microRNAs, piRNAs and lncRNAs. It comprises 12-13 subunits (13 in D. melanogaster), ten of which form a structurally conserved catalytic core with additional subunits located on the periphery. Notably, five RNAP II subunits are shared with the other two nuclear RNAPs. For transcription initiation, RNAPII assembles with the general transcription factors at promoter DNA to form the pre-initiation complex. (Adapted from FBrf0247389, FBrf0228779, FBrf0213652, PMID:25693126, PMID:23463798 and PMID:17318225.)
RNA POLYMERASE CATALYTIC SUBUNITS -
DNA-directed RNA polymerases (RNAPs) catalyze the synthesis of RNA from DNA templates. Nuclear DNA is transcribed by three different multi-subunit polymerases, RNAPs I, II and III, which synthesize mRNAs, rRNAs, tRNAs and other non-coding RNAs. Although composed of between 12-17 subunits, all three nuclear RNAPs contain a ten-subunit catalytic core. Mitochondrial RNA is synthesized by a single subunit RNA polymerase. DNA primases are a class of RNA polymerases that catalyse the synthesis of short RNA primers that are extended by DNA polymerases during DNA replication. (Adapted from PMID:22365827 and PMID:19540940.)
Protein Function (UniProtKB)
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template (By similarity).
(UniProt, P36958)
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Polr2I for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Gene model reviewed during 5.53

Gene model reviewed during 5.41

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082925
701
129
FBtr0309995
694
129
FBtr0346348
1035
129
Additional Transcript Data and Comments
Reported size (kB)

1.2, 0.85 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0082384
15.1
129
5.22
FBpp0301701
15.1
129
5.22
FBpp0312065
15.1
129
5.22
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

129 aa isoforms: Polr2I-PA, Polr2I-PB, Polr2I-PC
Additional Polypeptide Data and Comments
Reported size (kDa)

129 (aa); 15.1 (kD)

Comments
External Data
Subunit Structure (UniProtKB)

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.

(UniProt, P36958)
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Polr2I using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
No Assay Recorded
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

This is a minor Polr2I transcript present at all developmental times tested.

Polr2I transcripts are expressed in all developmental stages. They are expressed ubiquitously in embryos, larvae and adults.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Polr2I in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Polr2I
Transgenic constructs containing regulatory region of Polr2I
Aberrations (Deficiencies and Duplications) ( 13 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (9)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
2 of 15
No
No
1  
1 of 15
No
No
1 of 15
No
No
1  
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1  
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (10)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (11)
9 of 13
Yes
Yes
7 of 13
No
Yes
2 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (7)
3 of 12
Yes
Yes
2 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
Yes
1 of 12
No
No
Danio rerio (Zebrafish) (6)
14 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
15 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (2)
8 of 9
Yes
Yes
8 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (4)
14 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
11 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190HZK )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150FB6 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0J3P )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0J86 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0W1S )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (4)
3 of 10
3 of 10
1 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Interactions Browser
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
    (UniProt, P36958 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-55
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    88B3-88B3
    Limits computationally determined from genome sequence between P{lacW}trxj14A6&P{PZ}trx00347 and P{PZ}cv-c06951
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (15)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (77)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
    Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      BDGP DGC clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of

      Source for identity of: Polr2I RpII15

      Source for database merge of
      Additional comments
      Other Comments

      RNAi screen using dsRNA made from templates generated with primers directed against this gene results in aberrantly long spindles with misaligned chromosomes when assayed in S2 cells in the presence of Cdc27 dsRNA. This phenotype cannot be observed when the screen is performed without Cdc27 dsRNA.

      Used in a phylogenetic analysis, the tree in inferred by parsimony method from RpoB sequences, or homologous, multiple alignment.

      Designation as "RpII215" was in error.

      Isolation of the coding sequence and immunoblotting experiments demonstrate the RpII15 gene codes for a small subunit of RNA polymerase II.

      The technique of paramagnetic particle-mediated selection of terminated run-on transcripts was used to examine RNA polymerase II pausing and 5' cap formation at high resolution on the heat shock genes Hsp70A, Hsp70B, Hsp26 and Hsp27. Results demonstrate that polymerases pause over a narrow region of each heat shock gene, not at a defined point. 5' capping occurs over a region coincidental with that of pausing.

      Protein complexes of RNA polymerase II localise to major developmental puffs and heat shock puffs.

      RpII15 is an essential gene required maternally for embryogenesis.

      Origin and Etymology
      Discoverer
      Etymology

      Named 'Polr2I' after the human ortholog.

      Identification
      External Crossreferences and Linkouts ( 67 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      modMine - A data warehouse for the modENCODE project
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (25)
      Reported As
      Symbol Synonym
      RNAP
      l(3)88Be
      Secondary FlyBase IDs
        Datasets (1)
        Study focus (1)
        Experimental Role
        Project
        Project Type
        Title
        • bait_protein
        ChIP characterization of transcription factor genome binding, Berkeley Drosophila Transcription Factor Network Project.
        References (124)