FB2025_01 , released February 20, 2025
Gene: Dmel\Polr2D
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General Information
Symbol
Dmel\Polr2D
Species
D. melanogaster
Name
RNA polymerase II subunit D
Annotation Symbol
CG43662
Feature Type
protein_coding_gene
FlyBase ID
FBgn0263757
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Associates with POLR2G. (UniProt, Q9VEA5)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Rpb4, DmRPB4

Key Links
Genomic Location
Cytogenetic map
90F10-90F11
Sequence location
Recombination map
3-62
RefSeq locus
NT_033777 REGION:18252843..18255487
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with FLYBASE:Polr2G; FB:FBgn0051155
(Muratoglu et al., 2003)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables nucleotide binding
inferred from electronic annotation with InterPro:IPR010997
(InterPro Project Members, 2004-)
enables translation initiation factor binding
inferred from biological aspect of ancestor with PANTHER:PTN000480538
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in transcription by RNA polymerase II
inferred from direct assay
(Muratoglu et al., 2003)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in DNA-templated transcription initiation
inferred from electronic annotation with InterPro:IPR005574
(InterPro Project Members, 2004-)
involved_in transcription by RNA polymerase II
inferred from sequence or structural similarity with UniProtKB:O15514
(Gene Ontology Curators, 2002-)
inferred from sequence or structural similarity with HGNC:9191
(Aoyagi and Wassarman, 2000)
inferred from sequence or structural similarity with SGD:S000003676
(Aoyagi and Wassarman, 2000)
involved_in transcription initiation at RNA polymerase II promoter
inferred from biological aspect of ancestor with PANTHER:PTN000480538
(GO Reference Genome Project, 2011-)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
located_in polytene chromosome interband
inferred from direct assay
(Pankotai et al., 2010)
located_in polytene chromosome puff
inferred from direct assay
(Pankotai et al., 2010)
located_in polytene chromosome
inferred from direct assay
(Muratoglu et al., 2003)
part_of RNA polymerase II, core complex
inferred from direct assay
(Muratoglu et al., 2003)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of RNA polymerase complex
inferred from electronic annotation with InterPro:IPR005574
(InterPro Project Members, 2004-)
part_of RNA polymerase II, core complex
inferred from sequence or structural similarity with UniProtKB:O15514
(Gene Ontology Curators, 2002-)
inferred from sequence or structural similarity with HGNC:9191
(Aoyagi and Wassarman, 2000)
inferred from sequence or structural similarity with SGD:S000003676
(Aoyagi and Wassarman, 2000)
inferred from biological aspect of ancestor with PANTHER:PTN000480538
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the eukaryotic RPB4 RNA polymerase subunit family. (Q9VEA5)
Protein Signatures (InterPro)
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.)
Protein Function (UniProtKB)
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Associates with POLR2G.
(UniProt, Q9VEA5)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Polr2D 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 Q9VEA5)

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 5.42

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.47

Complete overlap: transcripts of this gene are completely overlapped by those of a second gene on the same strand.

Genes with CDS overlap: Rpb4 and Ada2a share promoter, first exon and N-terminal coding sequences (21 residues); overlapping structure not conserved outside of insects (see FBrf0209781).

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Polr2D-RF
FBtr0310379
NM_001014633
722
139
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
Polr2D-PF
FBpp0302530
16.2
139
4.46
Q9VEA5
NP_001014633
AAF55522
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

RNA polymerase II consists of 12 different subunits.

(UniProt, Q9VEA5)
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\Polr2D 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
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).

NA

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in polytene chromosome interband
inferred from direct assay
(Pankotai et al., 2010)
located_in polytene chromosome puff
inferred from direct assay
(Pankotai et al., 2010)
located_in polytene chromosome
inferred from direct assay
(Muratoglu et al., 2003)
part_of RNA polymerase II, core complex
inferred from direct assay
(Muratoglu et al., 2003)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Polr2D in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Polr2D
Transgenic constructs containing regulatory region of Polr2D
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene partially disrupted in
Df(3R)d189
(Komonyi et al., 2005)
Inferred from location ( 6 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\POLR2D
14 of 14
Yes
Yes
1  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Polr2d
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Polr2d
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\polr2d
10 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\polr2d
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\rpb-4
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP001228
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (3)
Atha\NRPB4
13 of 13
Yes
Yes
Atha\NRPD4
3 of 13
No
No
Atha\AT4G08545
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\RPB4
8 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\rpb4
10 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Polr2D. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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 ( 1 )
    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.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    POLR2D; RNA polymerase II subunit D
    14 of 14
    606017
         
        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
        Other Interaction Browsers
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        RNA polymerase II consists of 12 different subunits.
        (UniProt, Q9VEA5 )
        Linkouts
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-62
        Cytogenetic map
        90F10-90F11
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        90F10-90F11
        Limits computationally determined from genome sequence between P{EP}cpoEP3679 and P{EP}Dlc90FEP3634
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-62

        (FlyBase, 2016)

        3-61.9

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (9)
        Genomic Clones (23)
        cDNA Clones (9)
         

        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)
        BDGP DGC clones
          Other clones
          RNAi and Array Information
          Linkouts
          Antibody Information
          Laboratory Generated Antibodies
           

          polyclonal

          (Pankotai et al., 2010, Muratoglu et al., 2003)
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments

              Nonsense-mediated mRNA decay (NMD) down-regulates a distinct splice isoform(s) of this gene.

              (Hansen et al., 2009)

              Annotations CG31318 and CG31237 merged as CG33520 in release 4.1 of the genome annotation.

              (FlyBase Genome Annotators, 2005)
              Relationship to Other Genes
              Source for database merge of
              Additional comments

              Annotation CG33520 split into CG43662 (which corresponds to Rpb4) and CG43663 (which corresponds to Ada2a) in release 5.43 of the genome annotation.

              (FlyBase Genome Annotators, 2012)

              The Rpb4 and Ada2a loci share a common first exon, which results in the Rpb4 and Ada2a proteins sharing 21 amino acid residues at their N-terminal end.

              (Muratoglu et al., 2003)
              Nomenclature History
              Source for database identify of

              Source for identity of: Rpb4 CG7150

              (Aoyagi and Wassarman, 2000)

              Source for identity of: Polr2D Rpb4

              (Marygold et al., 2020)
              Nomenclature comments
              Etymology

              Named 'Polr2D' after the human ortholog.

              (Marygold et al., 2020)
              Synonyms and Secondary IDs (14)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 50 )
              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
              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
              InterPro - A database of protein families, domains and functional sites
              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
              Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              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 (protein-protein) - An integrated Molecular Interaction Database
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              References (53)