FlyBase Gene Report: Dmel\PolA2

General Information

Symbol

Dmel\PolA2

Species

D. melanogaster

Name

DNA polymerase alpha subunit 2

Annotation Symbol

CG5923

Feature Type

protein_coding_gene

FlyBase ID

FBgn0005696

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Snapshot

Contributions welcome

Other Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

DNApol-α73, DNA polymerase α, pol α, Polα, DNA polymerase alpha primase 73 kda subunit

Key Links

Genomic Location

Cytogenetic map

97E10-97E10

Sequence location

3R:27,239,163..27,241,228 [+]

Recombination map

3-92

RefSeq locus

NT_033777 REGION:27239163..27241228

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (7 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR007185

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables DNA-directed DNA polymerase activity

inferred from electronic annotation with InterPro:IPR007185

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in DNA-dependent DNA replication

inferred from direct assay

(Kuroda et al., 1990, Kaguni et al., 1983)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in DNA replication initiation

inferred from biological aspect of ancestor with PANTHER:PTN000551732

(assigned by GO_Central )

(Gaudet et al., 2011)

inferred from sequence or structural similarity with UniProtKB:P38121

(assigned by UniProt )

(UniProt Curators, 2002-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

part_of alpha DNA polymerase:primase complex

inferred from direct assay

(Kuroda et al., 1990, Kaguni et al., 1983, Kaguni et al., 1983)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

part_of alpha DNA polymerase:primase complex

inferred from biological aspect of ancestor with PANTHER:PTN000551732

(assigned by GO_Central )

(Gaudet et al., 2011)

inferred from sequence or structural similarity with UniProtKB:P38121

(assigned by UniProt )

(UniProt Curators, 2002-)

located_in nuclear envelope

inferred from sequence or structural similarity with UniProtKB:P38121

(assigned by UniProt )

(UniProt Curators, 2002-)

located_in nucleus

inferred from sequence or structural similarity with UniProtKB:P38121

(assigned by UniProt )

(UniProt Curators, 2002-)

Gene Group (FlyBase)

DNA POLYMERASE ALPHA-PRIMASE

Protein Family (UniProt)

Belongs to the DNA polymerase alpha subunit B family. (Q9VB62)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

DNA POLYMERASE ALPHA-PRIMASE -: DNA polymerase alpha-primase synthesizes short RNA-DNA primers on the lagging strand during DNA synthesis. It is a heterotetramer composed of two polymerase subunits (DNApol-α180 and DNApol-α73) and two primase subunits (DNApol-α50 and DNApol-α60). DNApol-α180 and DNApol-α50 encode the DNA polymerase and RNA primase catalytic activities, respectively, while DNApol-α73 and DNApol-α60 encode the regulatory subunits. (Adapted from PMID:30005324.)

Protein Function (UniProtKB)

Accessory subunit of the DNA polymerase alpha complex (also known as the alpha DNA polymerase-primase complex) which plays an essential role in the initiation of DNA synthesis (PubMed:6773966, PubMed:6403945, PubMed:6409898, PubMed:7592543). During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1/p180, an accessory subunit POLA2/p70 and two primase subunits, the catalytic subunit PRIM1/p49 and the regulatory subunit PRIM2/p58) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1 (By similarity). The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands. These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively (By similarity).

(UniProt, Q9VB62)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\PolA2 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

Comments on Gene Model

Gene model reviewed during 5.46

Gene model reviewed during 5.49

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

PolA2-RC

FBtr0114543

NM_170327

2066

609

Additional Transcript Data and Comments

Reported size (kB)

2.5 (northern blot)

(Cotterill et al., 1992)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

PolA2-PC

FBpp0113035

67.0

609

5.17

NP_733206

AAF56680

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)

653 (aa); 73 (kD observed)

(Cotterill et al., 1992)

Comments

External Data

Subunit Structure (UniProtKB)

Component of the alpha DNA polymerase complex (also known as the alpha DNA polymerase-primase complex) consisting of four subunits: the catalytic subunits DNApol-alpha50/DNAprim1 and DNApol-alpha180/DNApolA1 and the accessory subunits DNApol-alpha60/DNAprim2 and DNApol-alpha73/DNApolA2 (PubMed:6773966, PubMed:6403945, PubMed:6409898). DNApol-alpha180/DNApolA1 associates with the DNA primase complex before association with DNApol-alpha73/DNApolA2 (PubMed:6409898).

(UniProt, Q9VB62)

Post Translational Modification

Phosphorylated in embryos until cycle 13.

(UniProt, Q9VB62)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VB62

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\PolA2 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

DNApol-alpha73_1

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

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

fertilized egg stage

male pronucleus

• chromatin

Comment: interphase

(Loppin et al., 2001)

female pronucleus

• chromatin

Comment: interphase

(Loppin et al., 2001)

Additional Descriptive Data

mus209 and PolA2 proteins are detected associated with the nuclear chromatin of interphase apposed male and female pro-nuclei in newly fertilized eggs in preparation for the completion of DNA replication prior to the first zygotic division.

(Loppin et al., 2001)

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of alpha DNA polymerase:primase complex

inferred from direct assay

(Kuroda et al., 1990, Kaguni et al., 1983, Kaguni et al., 1983)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\PolA2 in GBrowse 2

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\PolA2

View exonic expression by tissue for Dmel\PolA2

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

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0005696

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG5923-RA

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG5923

Flygut - An atlas of the Drosophila adult midgut

FBgn0005696

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of PolA2

Transgenic constructs containing regulatory region of PolA2

Deletions and Duplications ( 2 )

Disrupted in

Df(3R)Exel6207

(Ryder, 2004.4.26)

Df(3R)Exel6208

(Ryder, 2004.4.26)

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

viable, with Scer\GAL4^Mef2.PR

PolA2^GD4243

Other Phenotypes

Allele

visible, with Scer\GAL4^ey.PU

PolA2^NIG.5923R

Phenotype manifest in

Allele

eye, with Scer\GAL4^ey.PU

PolA2^NIG.5923R

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\POLA2

15 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Pola2

14 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Pola2

13 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\pola2

13 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\pola2

14 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\div-1

12 of 15

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\POLA2

7 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\POL12

11 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\spb70

8 of 12

Yes

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091904O4 )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA19232

Drosophila persimilis

Dper\GL24481

Drosophila willistoni

Dwil\GK22573

Drosophila virilis

Dvir\GJ10668

Drosophila mojavensis

Dmoj\GI10451

Drosophila grimshawi

Dgri\GH16851

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091503SP )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17022123

Glossina morsitans

Tsetse fly

Gmor\GMOY003177

Mayetiola destructor

Hessian fly

Mdes\Mdes002680

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL007692

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL009905

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL001823

Anopheles gambiae

Malaria mosquito

Agam\AGAP004392

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ001712

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ001713

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04ME )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA005158

Danaus plexippus

Monarch butterfly

Dple\DPOGS204200-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL009900

Apis florea

Little honeybee

Aflo\2147488131

Apis mellifera

Western honey bee

Amel\GB44543

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP18824

Bombus terrestris

Buff-tailed bumblebee

Bter\15216608

Linepithema humile

Argentine ant

Lhum\LH23065

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:002691

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG011724

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_02205

Tribolium castaneum

Red flour beetle

Tcas\TC005585

Pediculus humanus

Human body louse

Phum\PHUM003740

Rhodnius prolixus

Kissing bug

Rpro\RPRC011417

Cimex lectularius

Bed bug

Clec\CLEC000692

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI008858

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_03651

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X07VJ )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Ixodes scapularis

Black-legged tick

Isca\ISCW002323

Stegodyphus mimosarum

African social velvet spider

Smim\KFM69638.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur19g00480

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_321802

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0C6I )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Pola2

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Pola2_1

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000003161

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000026330

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (0)

No records found.

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.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

POLA2; DNA polymerase alpha 2, accessory subunit

15 of 15

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

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

PolA2 - Dpit47

anti bait coimmunoprecipitation, western blot

(Crevel et al., 2001)

PolA2 - PolA1

ion exchange chromatography, molecular weight estimation by staining

(Kaguni et al., 1983)

PolA2 - Prim1

ion exchange chromatography, molecular weight estimation by staining

(Kaguni et al., 1983)

PolA2 - Prim2

ion exchange chromatography, molecular weight estimation by staining

(Kaguni et al., 1983)

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

Subunit Structure (UniProtKB)

(UniProt, Q9VB62 )

Linkouts

BioGRID - A database of protein and genetic interactions.

68166

DroID - A comprehensive database of gene and protein interactions.

FBgn0005696

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

43278

MIST (protein-protein) - An integrated Molecular Interaction Database

DNApol-alpha73

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-92

Cytogenetic map

97E10-97E10

Sequence location

3R:27,239,163..27,241,228 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

97E10-97E10

Limits computationally determined from genome sequence between P{PZ}sda⁰³⁸⁸⁴ and P{PZ}btz^rL203

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-92

(FlyBase, 2016)

3-90.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

Bloomington

77417

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06549}attP2

VDRC

v108579

P{KK101423}VIE-260B

Genomic Clones (12)

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

cDNA Clones (28)

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

GM08365

Other clones

FI22303

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.

FBgn0005696

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0005696

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

43278

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Cotterill et al., 1992)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: PolA2 DNApol-α73

(Marygold et al., 2020)

Source for database merge of

Additional comments

Other Comments

Analysis of DNApol-α73-Ecol\CAT deletion constructs shows that full promoter activity is located within the region from -285 to +129bp of DNApol-α73. Three DREs (DNA-replication related elements) are located within this region, and DNA footprinting analysis shows that Dref can bind to all three sites. Mutation of any one of the DRE sites causes extensive reductions in promoter activity and Dref binding to the promoter fragment.

(Takahashi et al., 1996)

A monoclonal antibody to the 72kD protein stains interphase nuclei, but not metaphase chromosomes. The protein is present in the embryo as a maternal product.

(Kuroda and Ueda, 1995)

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

(Mitsis et al., 1995)

Expression pattern and subcellular distribution of the protein during development is studied using antibodies.

(Yamaguchi et al., 1995)

The properties of the DNA polymerase α enzyme have been studied.

(Cai et al., 1993)

The gene for the 73kD subunit of the DNA polymerase α primase has been cloned and nucleotide sequence motifs constituting control regions have been analysed.

(Cotterill et al., 1992)

25bp DNA oligomer containing m⁴T is used in a gel extension assay to measure the efficiency of incorporation of dATP and dGTP opposite m⁴T using a DNA polymerase α-primase complex. The DNA polymerase α shows a clear preference for pairing with dGTP.

(Dosanjh et al., 1990)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 44 )

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.

43278

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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information