FB2025_01 , released February 20, 2025
Gene: Dmel\Polr2J
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General Information
Symbol
Dmel\Polr2J
Species
D. melanogaster
Name
RNA polymerase II subunit J
Annotation Symbol
CG6840
Feature Type
protein_coding_gene
FlyBase ID
FBgn0032634
Gene Model Status
Current
Stock Availability
7 publicly available
Enzyme Name (EC)
DNA-directed RNA polymerase (2.7.7.6)
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. RPB11 is part of the core element with the central large cleft (By similarity). (UniProt, Q9VJE4)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Rpb11

Key Links
Genomic Location
Cytogenetic map
36C7-36C7
Sequence location
Recombination map
2-53
RefSeq locus
NT_033779 REGION:17409698..17410406
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 (5 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables DNA binding
inferred from electronic annotation with InterPro:IPR008193
(InterPro Project Members, 2004-)
contributes_to DNA-directed 5'-3' RNA polymerase activity
inferred from sequence or structural similarity with HGNC:9187
(Aoyagi and Wassarman, 2000)
inferred from sequence or structural similarity with UniProtKB:P38902
(Aoyagi and Wassarman, 2000)
enables protein dimerization activity
inferred from electronic annotation with InterPro:IPR009025, InterPro:IPR036603
(InterPro Project Members, 2004-)
Biological Process (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in transcription by RNA polymerase II
inferred from sequence or structural similarity with UniProtKB:P38902
(Aoyagi and Wassarman, 2000)
inferred from biological aspect of ancestor with PANTHER:PTN000358883
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR037685
(InterPro Project Members, 2004-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of RNA polymerase II, core complex
inferred from sequence or structural similarity with UniProtKB:P38902
(Aoyagi and Wassarman, 2000)
inferred from biological aspect of ancestor with PANTHER:PTN000358883
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR037685
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA polymerase subunit family. (Q9VJE4)
Protein Signatures (InterPro)
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 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. RPB11 is part of the core element with the central large cleft (By similarity).
(UniProt, Q9VJE4)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Polr2J 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 Q9VJE4)

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

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

Gene model reviewed during 5.45

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Polr2J-RA
FBtr0081011
NM_135992
516
117
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
Polr2J-PA
FBpp0080564
13.4
117
5.23
Q9VJE4
NP_609836
AAF53606
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)

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

(UniProt, Q9VJE4)
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\Polr2J 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).

0.48

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
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\Polr2J 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
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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
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 Polr2J
Transgenic constructs containing regulatory region of Polr2J
Aberrations (Deficiencies and Duplications) ( 3 )
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
lethal, with Scer\GAL4pnr-MD237
lethal | pupal stage, with Scer\GAL4pnr-MD237
lethal | recessive
lethal - all die during P-stage, with Scer\GAL4Mef2.PR
partially lethal, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
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) (4)
Hsap\POLR2J
12 of 14
Yes
Yes
1  
Hsap\POLR2J2
10 of 14
No
Yes
Hsap\POLR2J3
9 of 14
No
Yes
Hsap\POLR1D
3 of 14
No
No
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\Polr2j
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (2)
Mmus\Polr2j
13 of 14
Yes
Yes
Mmus\Polr1d
3 of 14
No
No
Xenopus tropicalis (Western clawed frog) (3)
Xtro\polr1d.2
2 of 13
Yes
No
Xtro\polr2j
2 of 13
Yes
Yes
Xtro\fbxo8
1 of 13
No
No
Danio rerio (Zebrafish) (2)
Drer\polr2j
14 of 14
Yes
Yes
Drer\polr1d
3 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\rpb-11
14 of 14
Yes
Yes
Cele\rpac-19
3 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
Agam\RPB11_ANOGA
12 of 12
Yes
Yes
Agam\AgaP_AGAP009644
3 of 12
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\NRPB11
13 of 13
Yes
Yes
Atha\RPC14
3 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\RPB11
11 of 13
Yes
Yes
Scer\RPC19
2 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\rpb11
11 of 12
Yes
Yes
Spom\rpc19
2 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Polr2J. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
Polr1D
5 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.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    POLR2J; RNA polymerase II subunit J
    12 of 14
    604150
         
        POLR2J2; RNA polymerase II subunit J2
        10 of 14
        609881
            POLR2J3; RNA polymerase II subunit J3
            9 of 14
                POLR1D; RNA polymerase I and III subunit D
                3 of 14
                613715
                 
                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:
                Show/hide secondary interactors 
                (data from AllianceMine provided by esyN)
                Select Layout:
                Legend:
                Protein
                RNA
                Selected Interactor(s)
                Other Interaction Browsers
                View in FlyBase Interactions Browser   View in MIST tool (external link)
                Please see the Physical Interaction reports below for full details
                protein-protein
                Physical Interaction
                Assay
                References
                Polr2J - CG8117
                anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
                (Rhee et al., 2014)
                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)
                Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
                (UniProt, Q9VJE4 )
                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
                Class of Gene
                Genomic Location and Detailed Mapping Data
                Chromosome (arm)
                2L
                Recombination map
                2-53
                Cytogenetic map
                36C7-36C7
                Sequence location
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                36C7-36C7
                Limits computationally determined from genome sequence between P{lacW}Mhck10423&P{lacW}Cask03902 and P{lacW}Aac11k06710
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                Experimentally Determined Recombination Data
                Location

                2-53

                (FlyBase, 2016)

                2-52.7

                (Comeron et al., 2012)
                Left of (cM)
                Right of (cM)
                Notes
                Stocks and Reagents
                Stocks (7)
                Genomic Clones (12)
                 

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

                cDNA Clones (7)
                 

                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
                    DRSC - Results frm RNAi screens
                    Antibody Information
                    Laboratory Generated Antibodies
                     
                    Commercially Available Antibodies
                     
                    Cell Line Information
                    Publicly Available Cell Lines
                     
                      Other Stable Cell Lines
                       
                        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.

                        (Goshima et al., 2007)
                        Relationship to Other Genes
                        Source for database merge of

                        Source for merge of: Rpb11 BcDNA:GM15177

                        (FlyBase, 1996-)
                        Additional comments

                        Source for merge of Rpb11 BcDNA:GM15177 was a shared cDNA ( date:030728 ).

                        (FlyBase, 1996-)
                        Nomenclature History
                        Source for database identify of

                        Source for identity of: Rpb11 CG6840

                        (Aoyagi and Wassarman, 2000)

                        Source for identity of: Polr2J Rpb11

                        (Marygold et al., 2020)
                        Nomenclature comments
                        Etymology

                        Named 'Polr2J' after the human ortholog.

                        (Marygold et al., 2020)
                        Synonyms and Secondary IDs (6)
                        Datasets (0)
                        Study focus (0)
                        Experimental Role
                        Project
                        Project Type
                        Title
                        Study result (0)
                        Result
                        Result Type
                        Title
                        External Crossreferences and Linkouts ( 59 )
                        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.
                        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
                        FlyMine - An integrated database for Drosophila genomics
                        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
                        BioGRID - A database of protein and genetic interactions.
                        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                        DroID - A comprehensive database of gene and protein interactions.
                        DRSC - Results frm RNAi screens
                        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                        Flygut - An atlas of the Drosophila adult midgut
                        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 (protein-protein) - An integrated Molecular Interaction Database
                        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                        References (39)