FlyBase Gene Report: Dmel\phr

General Information

Symbol

Dmel\phr

Species

D. melanogaster

Name

photorepair

Annotation Symbol

CG11205

Feature Type

protein_coding_gene

FlyBase ID

FBgn0003082

Gene Model Status

Current

Stock Availability

6 publicly available

Enzyme Name (EC)

deoxyribodipyrimidine photo-lyase (4.1.99.3)

Gene Summary

photorepair (phr) encodes a DNA photolyase apoenzyme that repairs UV-induced DNA damage using FAD as a cofactor and blue light as a co-substrate. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Red Book
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

43E18-43E18

Sequence location

2R:7,825,289..7,827,319 [+]

Recombination map

2-57

RefSeq locus

NT_033778 REGION:7825289..7827319

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (3 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables deoxyribodipyrimidine photo-lyase activity

inferred from electronic annotation with InterPro:IPR008148

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000025285

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in DNA repair

inferred from electronic annotation with InterPro:IPR008148

(InterPro Project Members, 2004-)

involved_in photoreactive repair

inferred from biological aspect of ancestor with PANTHER:PTN000025285

(GO Reference Genome Project, 2011-)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

DNA PHOTOLYASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

deoxyribodipyrimidine photo-lyase activity

cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) (4.1.99.3)

RHEA 10672:

Summaries

Gene Snapshot

photorepair (phr) encodes a DNA photolyase apoenzyme that repairs UV-induced DNA damage using FAD as a cofactor and blue light as a co-substrate. [Date last reviewed: 2019-03-21]

Gene Group (FlyBase)

DNA PHOTOLYASES -: DNA photolyases are DNA repair enzymes that repair pyrimidine dimer DNA lesions cyclobutane pyrimidine dimers and 6,4 photoproducts caused by ultraviolet irradiation. (Adapted from FBrf0217122).

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

phr: photorepair

Deficient in photorepair of pyrimidine dimers; partially deficient in excision repair. Since phr/phr larvae show little or no photoreactivation after exposure to short wavelength UV light, the phr+ function is thought to play a significant role in UV resistance.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\phr 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 Q7JY97)

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 5.49

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

phr-RA

FBtr0088838

NM_078929

1915

555

phr-RB

FBtr0088839

NM_165564

1737

535

Additional Transcript Data and Comments

Reported size (kB)

2.070 (longest cDNA)

(Yasui et al., 1994)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

phr-PA

FBpp0087914

63.7

555

9.21

FBpp0087915

61.4

535

9.13

A1Z757

NP_724613

AAM68868

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

640 (aa); 74 (kD predicted)

(Yasui et al., 1994)

Comments

Proteins of 555 amino acids (64kD) or 535 amino acids (61kD) may be produced if downstream AUGs are utilized. The actual start codon remains to be determined. Photoreactivating activity was observed from phr protein expressed in E. coli.

(Yasui et al., 1994)

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\phr using the Feature Mapper tool.

External Data

Crossreferences

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

phr_1
phr_2

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).

2.43

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\phr in JBrowse

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

View exonic expression by developmental stage for Dmel\phr

View exonic expression by tissue for Dmel\phr

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

35735/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0003082

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003082

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0003082

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

CG11205

Flygut - An atlas of the Drosophila adult midgut

FBgn0003082

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of phr

Transgenic constructs containing regulatory region of phr

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

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

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

phr^GD12620

viable, with Scer\GAL4^Mef2.PR

phr^GD12620

viable, with Scer\GAL4^pnr-MD237

phr^GD12620

Other Phenotypes

Allele

abnormal DNA repair

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

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (3)

Hsap\CRY1

1 of 14

Yes

Hsap\CRY2

1 of 14

Yes

Hsap\TRMO

1 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (2)

Rnor\Cry2

2 of 14

Yes

Rnor\Cry1

1 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Cry2

2 of 14

Yes

Mmus\Cry1

1 of 14

Mmus\Trmo

1 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\phr

1 of 13

Yes

Xtro\trmo

1 of 13

Yes

Xtro\XB5887600

1 of 13

Yes

Danio rerio (Zebrafish) (8)

Drer\cpdp

13 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Drer\si:ch1073-390k14.1

1 of 14

Drer\trmo

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (4)

Agam\AgaP_AGAP005052

12 of 12

Yes

Agam\AgaP_AGAP008651

1 of 12

Agam\AgaP_AGAP012444

1 of 12

Agam\CRY1_ANOGA

1 of 12

Arabidopsis thaliana (thale-cress) (7)

Atha\PHR1

12 of 13

Yes

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\PHR1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (1)

Ecol\phr

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:phr. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (4)

CG18853

4 of 13

phr6-4

2 of 13

CG12822

1 of 13

cry

1 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?

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:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

MIST Molecular Interaction Search Tool

View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

phr - CG2889

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

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.

61601

DroID - A comprehensive database of gene and protein interactions.

FBgn0003082

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

35735

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-57

Cytogenetic map

43E18-43E18

Sequence location

2R:7,825,289..7,827,319 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

43E18-43E18

Limits computationally determined from genome sequence between P{EP}CanB2^EP774 and P{lacW}lin19^k01207&P{lacW}rnh1^k07624

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

44C-44D

(determined by in situ hybridisation)

(Todo et al., 1994)

43B-43C

(Hardin and Wensink, 1991)

Experimentally Determined Recombination Data

Location

2-57

(FlyBase, 2016)

2-57.2

(Comeron et al., 2012)

2-56.8

(Boyd and Harris, 1987)

Left of (cM)

(Boyd and Harris, 1987, Boyd and Harris, 1985)

Right of (cM)

(Boyd and Harris, 1987, Boyd and Harris, 1985)

Notes

Stocks and Reagents

Stocks (6)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

7046

phr^mus306-D1

63659

y¹ v¹; P{TRiP.HMJ30226}attP40/CyO

27676

y¹ v¹; P{TRiP.JF02755}attP2/TM3, Sb¹

NIG-Fly

HMJ30226

y¹ v¹; P{TRiP.HMJ30226}attP40/CyO

VDRC

v35497

w¹¹¹⁸; P{GD12620}v35497

v35499

w¹¹¹⁸; P{GD12620}v35499

Genomic Clones (14)

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

cDNA Clones (36)

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

RE21178

Other clones

DPiM_RE21178

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.

FBgn0003082

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0003082

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Gene is involved in pre-replication DNA repair of UV and AA lesions and photorepair.

(de Buendia, 1998)

Biochemical and photochemical characterisation of purified phr. Studies reveal the protein belongs to the folate class of enzymes.

(Kim et al., 1996)

Drosophila have two types of photolyase, the substrate of each photolyase is completely different. Photolyase repairs UV induced DNA damage, the two types of DNA damage are cyclobutane pyrimidine dimer (CPD) and (6-4) photoproduct. phr encodes the photolyase that specifically repairs CPD.

(Todo, 1996.4.30)

phr encodes the apoenzyme of DNA photolyase.

(Todo et al., 1994)

Transformation of E.coli SY2 cells with phr provides photoreactivity and increases survival of cells on illumination with visible light after UV irradiation.

(Yasui et al., 1994)

phr gene product preferentially binds to unusual DNA structures and is UV inducible.

(Hardin and Wensink, 1991)

Encodes a photolyase that repairs cyclobutane pyrimidine dimers induced by UV radiation of DNA.

Relationship to Other Genes

Source for database merge of

Source for merge of: phr anon-OV1

(Bayraktaroglu, 2000.11.2)

Additional comments

CG18853 appears to be a chimeric gene, with the 5' part of the gene derived from CG12822 and the 3' part of the gene derived from phr.

(Rogers and Hartl, 2012)

"CG18853" is a putative chimeric gene derived from the "CG12822" and "phr" genes (where coding sequences of the two parental genes contribute to the coding sequence of the chimeric gene).

(Rogers et al., 2009)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

C2PHR

(Kanai et al., 1997)

CG11205

(Rogers and Hartl, 2012, Zhan et al., 2011, Perkins et al., 2009)

CG11205-PA

(Rogers et al., 2009)

Dm CPD

(Todo, 1999)

PHR

(Deppisch et al., 2022)

Phl

anon-OV1

anonOV1

phr

(Xu et al., 2022, Lindsey et al., 2021, Sitnik et al., 2016, Fernández-Ayala et al., 2010, Kong et al., 2010, Rogers et al., 2009, Zraly et al., 2006)

Name Synonyms

CPD photolyase

DNA photolyase

(Yasui et al., 1994)

Photolyase

anonymous ovarian cDNA 1

photolyase

(Yasui, 1993.11.26)

photorepair

(Shen et al., 2013, Fernández-Ayala et al., 2010, Harbison et al., 2005)

Secondary FlyBase IDs

FBgn0011299
FBgn0014003

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 45 )

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.

35735

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.

Q7JY97

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.

Q7JY97

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

35735/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0003082

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0003082

FlyMine - An integrated database for Drosophila genomics

FBgn0003082

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

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG11205

MARRVEL_MODEL - MARRVEL (model organism gene)

35735

Linkouts

BioGRID - A database of protein and genetic interactions.

61601

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0003082

DroID - A comprehensive database of gene and protein interactions.

FBgn0003082

DRSC - Results frm RNAi screens

FBgn0003082

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

phr_1
phr_2

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003082

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0003082

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

CG11205

Flygut - An atlas of the Drosophila adult midgut

FBgn0003082

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

35735

References (60)

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

2.43

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