FB2025_01 , released February 20, 2025
Gene: Dmel\Polr2B
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General Information
Symbol
Dmel\Polr2B
Species
D. melanogaster
Name
RNA polymerase II subunit B
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 Summary
RNA polymerase II subunit B (Polr2B) encodes a protein thought to be present in all RNA pol II complexes. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
Also Known As

RNA polymerase II, RpII140, DmRP140, wimp, PolII

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-54
RefSeq locus
NT_033777 REGION:14125791..14130111
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (6 terms)
Molecular Function (3 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
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 sequence or structural similarity with UniProtKB:P08518
inferred from biological aspect of ancestor with PANTHER:PTN000466005
non-traceable author statement
Protein Family (UniProt)
Belongs to the RNA polymerase beta chain family. (P08266)
Catalytic Activity (EC/Rhea)
DNA-directed 5'-3' RNA polymerase activity
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate (2.7.7.6)
Summaries
Gene Snapshot
RNA polymerase II subunit B (Polr2B) encodes a protein thought to be present in all RNA pol II complexes. [Date last reviewed: 2019-03-14]
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. 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. Polr2B 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 (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 JBrowse view of Dmel\Polr2B 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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry P08266)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.54

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
UniProt
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: Polr2B-PA, Polr2B-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\Polr2B using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.43

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\Polr2B in JBrowse
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
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
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 54 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 15 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Polr2B
Transgenic constructs containing regulatory region of Polr2B
Aberrations (Deficiencies and Duplications) ( 21 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
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 v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
13 of 14
Yes
Yes
6 of 14
No
No
4 of 14
No
No
1  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
14 of 14
Yes
Yes
6 of 14
No
No
4 of 14
No
No
Mus musculus (laboratory mouse) (4)
14 of 14
Yes
Yes
6 of 14
No
No
3 of 14
No
No
1 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (5)
11 of 13
Yes
Yes
3 of 13
No
No
3 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
Danio rerio (Zebrafish) (4)
13 of 14
Yes
Yes
6 of 14
No
No
4 of 14
No
No
3 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (3)
14 of 14
Yes
Yes
6 of 14
No
No
4 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (6)
13 of 13
Yes
Yes
6 of 13
No
No
6 of 13
No
Yes
6 of 13
No
Yes
4 of 13
No
No
4 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (3)
13 of 13
Yes
Yes
5 of 13
No
No
3 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
12 of 12
Yes
Yes
5 of 12
No
No
3 of 12
No
No
Escherichia coli (enterobacterium) (1)
8 of 11
Yes
No
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Polr2B. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Drosophila melanogaster (Fruit fly) (2)
11 of 13
8 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    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 ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    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
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other Interaction Browsers

    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.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-54
    Cytogenetic map
    Sequence location
    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 JBrowse 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)
      RNAi and Array Information
      Linkouts
      Antibody Information
      Laboratory Generated Antibodies
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          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.

          Relationship to Other Genes
          Source for database merge of

          Source for merge of: RpII140 Rpb2

          Additional comments

          Mutants selected by Mortin, (1990) as extragenic suppressors of RpII215K1.

          Nomenclature History
          Source for database identify of

          Source for identity of: Polr2B RpII140

          Nomenclature comments
          Etymology

          Named 'Polr2B' after the human ortholog.

          Synonyms and Secondary IDs (43)
          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
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 70 )
          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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          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
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          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
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          MIST (genetic) - An integrated Molecular Interaction Database
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (197)