FB2024_02 , released April 23, 2024
Gene: Dmel\Polr3A
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General Information
Symbol
Dmel\Polr3A
Species
D. melanogaster
Name
RNA polymerase III subunit A
Annotation Symbol
CG17209
Feature Type
protein_coding_gene
FlyBase ID
FBgn0030687
Gene Model Status
Current
Stock Availability
6 publicly available
Enzyme Name (EC)
DNA-directed RNA polymerase (2.7.7.6)
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

dC160

Key Links
Genomic Location
Cytogenetic map
13E14-13E15
Sequence location
Recombination map
1-51
RefSeq locus
NC_004354 REGION:15762956..15769514
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 (8 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
(InterPro Project Members, 2004-)
enables DNA-directed 5'-3' RNA polymerase activity
(InterPro Project Members, 2004-)
contributes_to RNA polymerase III activity
inferred from biological aspect of ancestor with PANTHER:PTN000453625
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:P04051
(Gene Ontology Curators, 2002-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in positive regulation of transcription by RNA polymerase III
inferred from mutant phenotype
(Filer et al., 2017)
involved_in positive regulation of translation
inferred from mutant phenotype
(Filer et al., 2017)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in DNA-templated transcription
(InterPro Project Members, 2004-)
involved_in tRNA transcription by RNA polymerase III
inferred from sequence or structural similarity with UniProtKB:P04051
(Gene Ontology Curators, 2002-)
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 III complex
inferred from sequence or structural similarity with UniProtKB:P04051
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000453625
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
DNA-directed 5'-3' RNA polymerase activity
a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) (2.7.7.6)
Summaries
Gene Group (FlyBase)
RNA POLYMERASE III -
RNA polymerase III (RNAP III) synthesizes short, non-coding RNAs including tRNAs, the small 5S rRNA and the U6 snRNA. It comprises 17 subunits, ten of which form a structurally conserved catalytic core with additional subunits located on the periphery. Notably, five RNAP III subunits are shared among all three RNAPs and two others are shared between RNAPs I and III. (Adapted from FBrf0247389.)
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.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Polr3A 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 A8JUY3)

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 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Polr3A-RC
FBtr0300811
NM_001103517
4420
1383
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
Polr3A-PC
FBpp0290035
154.6
1383
8.70
A8JUY3
NP_001096987
ABW09418
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
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\Polr3A 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\Polr3A 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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Polr3A
Transgenic constructs containing regulatory region of Polr3A
Aberrations (Deficiencies and Duplications) ( 1 )
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) (4)
Hsap\POLR3A
14 of 14
Yes
Yes
Hsap\POLR2A
4 of 14
No
No
1  
Hsap\POLR1A
3 of 14
No
No
Hsap\UBXN7
1 of 14
No
No
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) (3)
Rnor\Polr3a
14 of 14
Yes
Yes
Rnor\Polr2a
5 of 14
No
No
Rnor\Polr1a
3 of 14
No
No
Mus musculus (laboratory mouse) (4)
Mmus\Polr3a
14 of 14
Yes
Yes
Mmus\Polr2a
5 of 14
No
No
Mmus\Polr1a
3 of 14
No
No
Mmus\Ubxn7
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (5)
Xtro\polr3a
11 of 13
Yes
Yes
Xtro\polr2a
2 of 13
No
No
Xtro\jak2
1 of 13
No
No
Xtro\polr1a
1 of 13
No
No
Xtro\tm6sf2
1 of 13
No
No
Danio rerio (Zebrafish) (4)
Drer\polr3a
13 of 14
Yes
Yes
Drer\polr2a
4 of 14
No
No
Drer\polr1a
2 of 14
No
No
Drer\ubxn7
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\rpc-1
14 of 14
Yes
Yes
Cele\ama-1
5 of 14
No
No
Cele\rpoa-1
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP004703
12 of 12
Yes
Yes
Agam\AgaP_AGAP007810
4 of 12
No
No
Arabidopsis thaliana (thale-cress) (6)
Atha\NRPC1
13 of 13
Yes
Yes
Atha\NRPB1
5 of 13
No
No
Atha\NRPA1
3 of 13
No
No
Atha\NRPD1A
3 of 13
No
No
Atha\NRPD1B
3 of 13
No
Yes
Atha\rpoC1
3 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\RPO31
13 of 13
Yes
Yes
Scer\RPO21
4 of 13
No
No
Scer\RPA190
2 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\rpc1
12 of 12
Yes
Yes
Spom\rpb1
4 of 12
No
No
Spom\nuc1
2 of 12
No
No
Escherichia coli (enterobacterium) (1)
Ecol\rpoC
9 of 11
Yes
No
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Polr3A. 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) (2)
Polr2A
10 of 13
Polr1A
7 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 ( 2 )
    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?
    POLR3A; RNA polymerase III subunit A
    14 of 14
    614258
    POLR2A; RNA polymerase II subunit A
    4 of 14
    180660
       
      POLR1A; RNA polymerase I subunit A
      3 of 14
      616404
      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
      MIST Molecular Interaction Search Tool
      Summary of Genetic Interactions
      esyN Network Diagram
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      External Data
      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
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-51
      Cytogenetic map
      13E14-13E15
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      13E14-13E15
      Limits computationally determined from genome sequence between P{EP}EP1489 and P{EP}BEST:RE35685EP1581&P{EP}sdEP1088
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      1-51

      (FlyBase, 2016)

      1-51.9

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (6)
      Genomic Clones (8)
       

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

      cDNA Clones (27)
       

      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
            Relationship to Other Genes
            Source for database merge of
            Additional comments
            Nomenclature History
            Source for database identify of

            Source for identity of: Rpc160 CG17209

            (Filer et al., 2017)

            Source for identity of: Polr3A Rpc160

            (Marygold et al., 2020)
            Nomenclature comments
            Etymology

            Named 'Polr3A' after the human ortholog.

            (Marygold et al., 2020)
            Synonyms and Secondary IDs (10)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 41 )
            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/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
            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.
            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 (38)