FB2021_02, released April 13, 2021

Gene: Dmel\phr6-4

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General Information
Symbol
Dmel\phr6-4
Species
D. melanogaster
Name
(6-4)-photolyase
Annotation Symbol
CG2488
Feature Type
protein_coding_gene
FlyBase ID
FBgn0016054
Gene Model Status
Current
Stock Availability
3 publicly available
Gene Summary
(6-4)-photolyase (phr6-4) encodes an enzyme that repairs DNA damage induced by ultraviolet light. It uses blue light and cofactor FADH to reverse the pyrimidine(6-4)pyrimidone photoproduct. [Date last reviewed: 2019-09-26] (FlyBase Gene Snapshot)
All Summaries
Also Known As

38D.25, 6-4 photolyase

Key Links
Genomic Location
Cytogenetic map
38D2-38D2
Sequence location
2L:20,643,351..20,645,791 [-]
Recombination map
2-54
RefSeq locus
NT_033779 REGION:20643351..20645791
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (7 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 deoxyribodipyrimidine photo-lyase activity
inferred from sequence or structural similarity with UniProtKB:P05066
(FlyBase Curators, 2008--)
enables DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000155848
(assigned by GO_Central )
(Gaudet et al., 2011)
enables FAD binding
inferred from biological aspect of ancestor with PANTHER:PTN000155848
(assigned by GO_Central )
(Gaudet et al., 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 circadian regulation of gene expression
inferred from biological aspect of ancestor with PANTHER:PTN002479144
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in entrainment of circadian clock by photoperiod
inferred from biological aspect of ancestor with PANTHER:PTN002479144
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN002479144
(assigned by GO_Central )
(Gaudet et al., 2011)
located_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN002479144
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
(6-4)-photolyase (phr6-4) encodes an enzyme that repairs DNA damage induced by ultraviolet light. It uses blue light and cofactor FADH to reverse the pyrimidine(6-4)pyrimidone photoproduct. [Date last reviewed: 2019-09-26]
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).
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\phr6-4 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 5.48

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
phr6-4-RA
FBtr0081404
NM_165334
2106
540
phr6-4-RB
FBtr0081405
NM_057840
2161
540
phr6-4-RC
FBtr0336829
NM_001273703
2044
540
phr6-4-RD
FBtr0336830
NM_001273704
1989
540
Additional Transcript Data and Comments
Reported size (kB)

2.0 (northern blot)

(Todo et al., 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
phr6-4-PA
FBpp0080934
62.5
540
9.81
NP_724274
AAN11080
phr6-4-PB
FBpp0080935
62.5
540
9.81
NP_477188
AAF53904
phr6-4-PC
FBpp0307793
62.5
540
9.81
NP_001260632
AGB93167
phr6-4-PD
FBpp0307794
62.5
540
9.81
NP_001260633
AGB93168
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

540 aa isoforms: phr6-4-PA, phr6-4-PB, phr6-4-PC, phr6-4-PD
Additional Polypeptide Data and Comments
Reported size (kDa)

540 (aa); 62.9 (kD predicted)

(Todo et al., 1996)
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\phr6-4 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
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\phr6-4 in GBrowse 2
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
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 ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of phr6-4
Transgenic constructs containing regulatory region of phr6-4
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2L)Exel7078
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\CRY2
8 of 15
Yes
Yes
Hsap\CRY1
7 of 15
No
Yes
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Cry1
7 of 15
Yes
Yes
0  
Mmus\Cry2
7 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Cry1
6 of 13
Yes
Yes
Rnor\Cry2
6 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (6)
Xtro\cry4
4 of 12
Yes
Yes
Xtro\cry1
3 of 12
No
Yes
Xtro\cry2
3 of 12
No
Yes
Xtro\LOC100144974
3 of 12
No
Yes
Xtro\cry-dash
2 of 12
No
Yes
Xtro\LOC100486741
1 of 12
No
Yes
Danio rerio (Zebrafish) (10)
Drer\cry5
14 of 15
Yes
Yes
Drer\cry1a
7 of 15
No
Yes
Drer\cry3a
6 of 15
No
Yes
Drer\cry2
5 of 15
No
Yes
Drer\cry4
5 of 15
No
Yes
Drer\cry3b
4 of 15
No
Yes
Drer\cry1b
3 of 15
No
Yes
Drer\cry-dash
3 of 15
No
Yes
Drer\si:ch1073-390k14.1
3 of 15
No
Yes
Drer\zgc:66475
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (5)
Atha\UVR3
9 of 9
Yes
Yes
Atha\CRY1
2 of 9
No
Yes
Atha\CRY2
2 of 9
No
Yes
Atha\CRY3
1 of 9
No
Yes
Atha\PHR2
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\PHR1
8 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091905FM )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00000834
Drosophila simulans
Dsim\GD21692
Drosophila sechellia
Dsec\GM23319
Drosophila erecta
Dere\GG21562
Drosophila yakuba
Dyak\GE12583
Drosophila ananassae
Dana\GF14557
Drosophila pseudoobscura pseudoobscura
Dpse\GA15376
Drosophila persimilis
Dper\GL19603
Drosophila willistoni
Dwil\GK15094
Drosophila virilis
Dvir\GJ17431
Drosophila mojavensis
Dmoj\GI19664
Drosophila grimshawi
Dgri\GH10854
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915038T )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17016987
Glossina morsitans
Tsetse fly
Gmor\GMOY002879
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07385
Mayetiola destructor
Hessian fly
Mdes\Mdes011832
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL001175
Anopheles darlingi
American malaria mosquito
Adar\ADAC010633
Anopheles gambiae
Malaria mosquito
Agam\AGAP008651
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ017734
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02F9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA000221
Bombyx mori
Silkmoth
Bmor\BGIBMGA007789
Danaus plexippus
Monarch butterfly
Dple\DPOGS210113-PA
Danaus plexippus
Monarch butterfly
Dple\DPOGS208079-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL005063
Heliconius melpomene
Postman butterfly
Hmel\HMEL003346
Apis florea
Little honeybee
Aflo\2380407668
Apis mellifera
Western honey bee
Amel\cry2
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP15161
Linepithema humile
Argentine ant
Lhum\LH14904
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0025ad
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG006626
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_06087
Tribolium castaneum
Red flour beetle
Tcas\cry2
Pediculus humanus
Human body louse
Phum\PHUM490060
Rhodnius prolixus
Kissing bug
Rpro\RPRC017361
Cimex lectularius
Bed bug
Clec\CLEC025215
Acyrthosiphon pisum
Pea aphid
Apim\cry2-2
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI087167
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI003810
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01703
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X02CO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ixodes scapularis
Black-legged tick
Isca\ISCW011472
Stegodyphus mimosarum
African social velvet spider
Smim\KFM80671.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM58835.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM60830.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM80670.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur09g05920
Tetranychus urticae
Two-spotted spider mite
Turt\tetur16g02770
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_195559
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_305792
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_300463
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G07M3 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Cry2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_018346gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Cry1/2L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Cry1
Gallus gallus
Domestic chicken
Ggal\CRY1
Gallus gallus
Domestic chicken
Ggal\LOC395100
Gallus gallus
Domestic chicken
Ggal\CRY2
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (3)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
cry
7 of 10
CG18853
1 of 10
phr
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.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    CRY2; cryptochrome circadian regulator 2
    8 of 15
    603732
        CRY1; cryptochrome circadian regulator 1
        7 of 15
        601933
           
          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
          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
          DroID - A comprehensive database of gene and protein interactions.
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          Pathways
          Signaling Pathways (FlyBase)
          Metabolic Pathways
          External Data
          Linkouts
          Genomic Location and Detailed Mapping Data
          Chromosome (arm)
          2L
          Recombination map
          2-54
          Cytogenetic map
          38D2-38D2
          Sequence location
          2L:20,643,351..20,645,791 [-]
          FlyBase Computed Cytological Location
          Cytogenetic map
          Evidence for location
          38D2-38D2
          Limits computationally determined from genome sequence between P{lacW}k02501&P{lacW}k14810 and P{PZ}Hr3802306&P{PZ}dia1
          Experimentally Determined Cytological Location
          Cytogenetic map
          Notes
          References
          39B-39C
          (determined by in situ hybridisation)
          (Todo et al., 1996)
          Experimentally Determined Recombination Data
          Location

          2-54

          (FlyBase, 2016)

          2-54.1

          (Comeron et al., 2012)

          2-

          Left of (cM)
          Right of (cM)
          Notes
          Stocks and Reagents
          Stocks (3)
          Genomic Clones (15)
           

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

          cDNA Clones (26)
           

          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)
          BDGP DGC clones
          Other clones
          RNAi and Array Information
          Linkouts
          DRSC - Results frm RNAi screens
          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: phr6-4 CG2488

          (Adams, 1999.11)
          Source for database merge of
          Additional comments
          Other Comments

          Gene is involved in pre-replication DNA photorepair.

          (de Buendia, 1998)

          phr6-4 enzyme can photorepair C6,4C, as well as T6,4T and T6,4C in vitro.

          (Todo et al., 1997)

          The action mechanism of phr6-4 with regard to binding specificity and catalytic mechanism by using conventional substrates, substrate analogs and presumed transition state analogs. The protein binds to its substrate and repairs it by a mechanism quite similar to the recognition and repair of Pyr<>Pyr by its cognate photolyase.

          (Zhao et al., 1997)

          phr6-4 has been cloned by functional complementation in E.coli.

          (Todo 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. phr6-4 encodes the photolyase that specifically repairs (6-4) photoproduct.

          (Todo, 1996.4.30)

          The properties of the phr6-4 enzyme have been analysed.

          (Kim et al., 1994)

          An enzyme that catalyses the light-dependent repair of (6-4) photoproduct exists in D.melanogaster.

          (Todo et al., 1993)

          Encodes a photolyase that repairs (6-4) photoproduct induced by UV radiation of DNA.

          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 46 )
          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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          modMine - A data warehouse for the modENCODE project
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyMine - An integrated database for Drosophila genomics
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          Synonyms and Secondary IDs (12)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (48)