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General Information
Symbol
Dmel\PolD1
Species
D. melanogaster
Name
DNA polymerase delta subunit 1
Annotation Symbol
CG5949
Feature Type
FlyBase ID
FBgn0263600
Gene Model Status
Stock Availability
Enzyme Name (EC)
DNA-directed DNA polymerase (2.7.7.7)
Gene Summary
As the catalytic component of the DNA polymerase delta complex, plays a crucial role in high fidelity genome replication, including lagging strand synthesis, DNA recombination and repair (By similarity). Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:7907087, PubMed:8415662, PubMed:1360647). Required at the nucleus of rapidly dividing embryonic cells to activate genome replication during the earliest cell cycles (PubMed:31100062). Likely to require the presence of accessory proteins PolD2 and PolD3 for full activity (PubMed:31100062). (UniProt, P54358)
Contribute a Gene Snapshot for this gene.
Also Known As

DNApol-delta, DNApol-δ, DNA polymerase delta, DNA-polymerase-δ, Polδ

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-43
RefSeq locus
NT_037436 REGION:15984322..15987815
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (12 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:Q9VIT0
(assigned by UniProt )
inferred from physical interaction with UniProtKB:Q9W088,UniProtKB:Q9Y118
(assigned by UniProt )
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000035478
(assigned by GO_Central )
enables DNA binding
inferred from electronic annotation with InterPro:IPR006134
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000035346
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR006134, InterPro:IPR006172, InterPro:IPR017964
(assigned by InterPro )
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000035478
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000035478
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000035346
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000035478
(assigned by GO_Central )
Cellular Component (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in nucleoplasm
inferred from direct assay
(assigned by UniProt )
located_in nucleus
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000035478
(assigned by GO_Central )
Protein Family (UniProt)
Belongs to the DNA polymerase type-B family. (P54358)
Catalytic Activity (EC)
Experimental Evidence
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (2.7.7.7)
Predictions / Assertions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (2.7.7.7)
Summaries
Gene Group (FlyBase)
DNA POLYMERASE DELTA -
DNA polymerase delta functions as a leading strand polymerase during nuclear DNA synthesis. It is a multi-subunit enzyme in which DNApol-δ encodes the catalytic subunit with polymerase and 3'-5' exonuclease proofreading activities. (Adapted from PMID:30005324.)
DNA POLYMERASE CATALYTIC SUBUNITS -
Multiple DNA polymerases are required for DNA replication and/or repair in eukaryotic cells. The alpha-primase, delta, epsilon, zeta and gamma polymerases exist as multi-subunit complexes in which one of the subunits has catalytic activity, whereas other DNA polymerases act as single molecules. (Adapted from PMID:30005324.)
3'-5'-EXODEOXYRIBONUCLEASES -
3'-5'-exodeoxyribonucleases catalyze the sequential degradation of double-stranded DNA acting progressively in a 3'-to-5' direction, releasing nucleoside 5'-phosphates.
Protein Function (UniProtKB)
As the catalytic component of the DNA polymerase delta complex, plays a crucial role in high fidelity genome replication, including lagging strand synthesis, DNA recombination and repair (By similarity). Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:7907087, PubMed:8415662, PubMed:1360647). Required at the nucleus of rapidly dividing embryonic cells to activate genome replication during the earliest cell cycles (PubMed:31100062). Likely to require the presence of accessory proteins PolD2 and PolD3 for full activity (PubMed:31100062).
(UniProt, P54358)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\PolD1 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry P54358)

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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.

Comments on Gene Model

Gene model reviewed during 5.44

Gene model reviewed during 5.46

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0075522
3440
1092
Additional Transcript Data and Comments
Reported size (kB)

4 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0075277
124.9
1092
6.90
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)

1092 (aa); 120 (kD observed); 125 (kD predicted)

Comments

The DNApol-δ protein sequence contains a number of homology boxes and conserved residues that are characteristic of δ DNA polymerases. Insect cells infected with the DNApol-δ cDNA show increased DNA polymerase activity.

External Data
Subunit Structure (UniProtKB)

Catalytic component of the DNA polymerase delta complex consisting of three subunits: the catalytic subunit PolD1 and two accessory subunits PolD2/Pol31 and PolD3/Pol32 (PubMed:31100062). Within the delta complex, interacts with both PolD2 and PolD3, and is able to interact with PolD2 in the absence of PolD3 (PubMed:31100062). Interacts with PCNA AND PCNA2 (PubMed:17087725).

(UniProt, P54358)
Domain

The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes.

(UniProt, P54358)
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\PolD1 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

antennal anlage

Comment: reported as procephalic ectoderm anlage

central brain anlage

Comment: reported as procephalic ectoderm anlage

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

visual anlage

Comment: reported as procephalic ectoderm anlage

ventral nerve cord primordium

Comment: reported as ventral nerve cord anlage

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleoplasm
inferred from direct assay
(assigned by UniProt )
located_in nucleus
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\PolD1 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
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 ( 15 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of PolD1
Transgenic constructs containing regulatory region of PolD1
Aberrations (Deficiencies and Duplications) ( 14 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
13 of 13
Yes
Yes
2 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (5)
9 of 12
Yes
Yes
2 of 12
No
No
1 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (4)
10 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
15 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (2)
9 of 9
Yes
Yes
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (4)
14 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
11 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (3)
3 of 10
2 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 v8.0 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
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    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)
    Catalytic component of the DNA polymerase delta complex consisting of three subunits: the catalytic subunit PolD1 and two accessory subunits PolD2/Pol31 and PolD3/Pol32 (PubMed:31100062). Within the delta complex, interacts with both PolD2 and PolD3, and is able to interact with PolD2 in the absence of PolD3 (PubMed:31100062). Interacts with PCNA AND PCNA2 (PubMed:17087725).
    (UniProt, P54358 )
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-43
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    72C1-72C1
    Limits computationally determined from genome sequence between P{EP}Tfb2EP572 and P{lacW}thj5C8&P{PZ}Mbs03802; Left limit from inclusion within Df(3L)Q26 (FBrf0085566) Right limit from non-inclusion within Df(3L)st-f13 (FBrf0072686)
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-[43]

    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (8)
    Genomic Clones (8)
     

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

    cDNA Clones (85)
     

    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 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
      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 identity of: PolD1 DNApol-δ

      Source for database merge of

      Source for merge of: DNApol-δ l(3)72Ac

      Additional comments
      Other Comments

      The 'l(3)72Ac' (DNApol-δ) complementation group comprises 13 EMS-induced mutant alleles.

      Cloning and characterisation of DNApol-δ reveals the amino acid sequence is very highly conserved.

      Subunits of DNA polymerase α and δ are purified from embryos and characterised.

      DNA polymerase δ has been isolated to near homogeneity from early embryos of D.melanogaster. The enzyme is composed of two polypeptides, which are 138kD and 47kD in size. The enzyme responds to mouse PCNA and has proofreading nuclease activity.

      DNApol-δ has been purified from 0-2hr embryos, it consists of a 120kD polypeptide and, unlike mammalian Polδ, is unresponsive to proliferating cell nuclear antigen (PCNA).

      Mono Q anion exchange chromatography used to resolve DNA polymerase activities in 0-2.5hr embryos. DNApol-δ and DNApol-α180 distinguished by copurification with DNAprimase (DNApol-α180) or 3'-5'exonuclease activity (DNApol-δ), immunoblot analysis with DNApol-α specific antibodies, sensitivity to aphidicolin (both DNApol-α180 and DNApol-δ sensitive) and BuPdGTP (DNApol-α180 more sensitive), and processivity measurements with and without PCNA (DNApol-δ has PCNA-inducible high processivity).

      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 49 )
      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
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      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
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      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
      FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
      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.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Synonyms and Secondary IDs (22)
      Datasets (8)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (8)
      Result
      Result Type
      Title
      Clustering analysis of hemocytes from non-infested third instar larvae
      Clustering analysis of hemocytes from wasp-infested third instar larvae
      Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
      Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
      Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
      Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
      Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
      Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
      References (78)