General Information
Symbol
Dmel\RpII140
Species
D. melanogaster
Name
RNA polymerase II 140kD subunit
Annotation Symbol
CG3180
Feature Type
FlyBase ID
FBgn0262955
Gene Model Status
Stock Availability
Enzyme Name (EC)
DNA-directed RNA polymerase (2.7.7.6)
Gene Snapshot
RNA polymerase II 140kD subunit has catalytic activity and is thought to be present in all RNA pol II complexes. [Date last reviewed: 2016-09-15]
Also Known As
DmRP140, wimp, Pol II, PolII, RNA Pol II
Genomic Location
Cytogenetic map
Sequence location
3R:14,125,791..14,130,111 [+]
Recombination map
3-54
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
Belongs to the RNA polymerase beta chain family. (P08266)
Molecular Function (see GO section for details)
Experimental Evidence
-
Predictions / Assertions
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1) (2.7.7.6)
Summaries
Gene Group Membership
RNA POLYMERASE II -
The RNA Polymerase II (RNAPII) is a multi-subunit enzyme that transcribes protein-coding genes to produce mRNAs. RNAPII also transcribes various other types of RNAs, including snRNA, small nucleolar RNA (snoRNA), microRNA, piRNA and long noncoding RNA. For transcription initiation, RNAPII assembles with the general transcription factors at promoter DNA to form the pre-initiation complex. (Adapted from FBrf0228779, FBrf0213652, PMID:25693126, PMID:23463798 and PMID:17318225).
UniProt Contributed Function Data
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. 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. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template (By similarity).
(UniProt, P08266)
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
RpII140: RNA polymeraseII-140 kd subunit
The structural gene for the 140-kd subunit of RNA polymerase II [RNA nucleotidyl transferase (EC 2.7.7.6)]. The gene is highly conserved judging from shared sequence homology with the yeast 150-kd subunit gene.
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\RpII140 or the JBrowse view of Dmel\RpII140 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 5.54
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082892
3775
1176
FBtr0344600
4060
1176
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0082353
134.0
1176
7.04
FBpp0310926
134.0
1176
7.04
Polypeptides with Identical Sequences

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

1176 aa isoforms: RpII140-PA, RpII140-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
(UniProt, P08266)
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\RpII140 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Gene Ontology (6 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
non-traceable author statement
(assigned by UniProt )
inferred from biological aspect of ancestor with PANTHER:PTN000465875
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR015712
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000466005
(assigned by GO_Central )
Biological Process (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
non-traceable author statement
(assigned by UniProt )
inferred from sequence or structural similarity with HGNC:9188
inferred from sequence or structural similarity with SGD:S000005677
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000466005
(assigned by GO_Central )
inferred from sequence or structural similarity with HGNC:9188
inferred from sequence or structural similarity with SGD:S000005677
non-traceable author statement
(assigned by UniProt )
Expression Data
Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\RpII140 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 54 )
For All Classical and Insertion Alleles Show
 
Allele of RpII140
Class
Mutagen
Associated Insertion
Stocks
Known lesion
Other relevant insertions
Transgenic Constructs ( 14 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of RpII140
Allele of RpII140
Mutagen
Associated Transgenic Construct
Stocks
Transgenic constructs containing regulatory region of RpII140
reporter construct
Name
Expression Data
Deletions and Duplications ( 21 )
Summary of Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
2 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
2 of 15
No
No
Rattus norvegicus (Norway rat) (2)
13 of 13
Yes
Yes
2 of 13
No
No
Xenopus tropicalis (Western clawed frog) (1)
8 of 12
Yes
Yes
Danio rerio (Zebrafish) (3)
10 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (3)
13 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (4)
9 of 9
Yes
Yes
2 of 9
No
No
2 of 9
No
Yes
2 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
15 of 15
Yes
Yes
2 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
12 of 12
Yes
Yes
2 of 12
No
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091900Z4 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
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
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500LE )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House 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) ( EOG090W00HJ )
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
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
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
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00GO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00RQ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    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
    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
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please look at the Interaction Group reports for full details of the physical interactions
    protein-protein
    Interacting group
    Assay
    References
    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, P08266 )
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    Pathways
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-54
    Cytogenetic map
    Sequence location
    3R:14,125,791..14,130,111 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    88A9-88A9
    Limits computationally determined from genome sequence between P{PZ}flfl01949 and P{lacW}trxj14A6&P{PZ}trx00347
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    88A10-88A10
    (determined by in situ hybridisation)
    88A-88B
    (determined by in situ hybridisation)
    88A10-88B2
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (15)
    Genomic Clones (22)
    cDNA Clones (82)
     

    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 sequences
    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)
      RNAi and Array Information
      Linkouts
      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 database merge of
      Source for merge of: RpII140 Rpb2
      Additional comments
      Mutants selected by Mortin, (1990) as extragenic suppressors of RpII215K1.
      Other Comments
      DNA-protein interactions: genome-wide binding profile (ChIP-chip) assayed for PolII holoenzyme in adult heads; see GEO_GSE32613 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32613).
      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.
      Suppressor mutations isolated on the basis of restoring viability to RpII215 and RpII140 mutants identify discrete domains in either subunit. The suppressor domain is required for viability and functioning of RNA polymerase II. The mutations recovered are not random and might provide insights into possible mechanisms for mutagenesis in eukaryotes.
      Used in a phylogenetic analysis, the tree in inferred by parsimony method from RpoB sequences, or homologous, multiple alignment.
      Sequences important for the transcription of RpII140 are located in the untranslated leader of the divergently transcribed 140up gene.
      Deletion analysis of the RpII140 protein shows that a region in the N-terminal part of the protein (amino acids 357-504) shows strong DNA binding, and the C-terminal part of the protein (amino acids 860-1160) shows some weak DNA binding.
      Ecol\lacZ RpII140 fusion proteins expressing overlapping fragments of RpII140 identify a protein segment that has the potential to bind DNA nonspecifically.
      Upstream of RpII140 is a gene, 140up, which is transcribed in the opposite direction. Both genes are characterised by multiple transcription start sites. Gel retardation assays with in vitro transcribed and translated Tbp reveals two regions in the RpII140 promoter region that bind Tbp. Transient transfection assays with Tbp and Ecol\CAT driven by the RpII140 promoter result in 2-3 fold increase in Ecol\CAT activity, promoter deletion analysis identifies three regions important for transcription.
      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.
      Three RpII140 alleles cause a dominant enhancement of the Ubx effect: transformation of the capitellum to wing. The alleles do not enhance the Ubx effect of RpII15 alleles.
      The initiating ATGs of the divergently transcribed 140up and RpII140 are only 467bp apart, and a central 309bp fragment from this region can direct transcription in either orientation.
      A TATA-dependent protein-DNA complex is found in fractionated embryonic nuclear extracts. DNase I footprint analysis identifies polypeptides (including Taf12, Tbp and RpII140) that require the Hsp70Bb TATA element for binding to regions of the Hsp70Bb promoter.
      RpII140 has been cloned and sequenced.
      The structural gene for the 140kD subunit of RNA polymerase II (RNA nucleotidyl transferase). The gene is highly conserved judging from shared sequence homology with the yeast 150kD subunit gene.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 63 )
      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
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      Linkouts
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
      DroID - A comprehensive database of gene and protein interactions.
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      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.
      Synonyms and Secondary IDs (39)
      Reported As
      Symbol Synonym
      RNA Pol II 140
      RNAP
      l(3)RplII140
      Secondary FlyBase IDs
      • FBgn0003276
      • FBgn0083157
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (181)