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Gene Dmel\phr6-4

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	1 publicly available
Also Known As	38D.25
Genomic Location
Chromosome (arm)	2L	Recombination map	2-
Cytogenetic map	38D2-38D2	Sequence location	2L:20,643,351..20,645,791 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents Beta	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene (6-4)-photolyase is referred to in FlyBase by the symbol Dmel\phr6-4 (CG2488, FBgn0016054). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: DNA (6-4) photolyase activity. Based on sequence similarity, it is predicted to be involved in the biological process: DNA repair. 5 alleles are reported. No phenotypic data is available. It has 4 annotated transcripts and 4 annotated polypeptides. Protein features are: DNA photolyase, FAD-binding/Cryptochrome, C-terminal; DNA photolyase, N-terminal; Rossmann-like alpha/beta/alpha sandwich fold. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult testis. Comments on Affy2 ProbeSet: ProbeSet 1635020_s_at completely aligns to an exonic region common to each of the 2 FlyBase-annotated transcript isoforms of phr6-4. Gene sequence location is 2L:20643351..20645791.
User Contributed Data
	Beta version, feedback welcome
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
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-
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\phr6-4 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene model reviewed during 5.48
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated 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 & 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 protein 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
Additional Polypeptide Data & Comments
Reported size (kDa)	540 (aa); 62.9 (kD predicted) (Todo et al., 1996)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • DNA photolyase, FAD-binding/Cryptochrome, C-terminal (IPR005101) DNA photolyase, N-terminal (IPR006050) Rossmann-like alpha/beta/alpha sandwich fold (IPR014729)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA695572   AE014134 AAF53904   AE014134 AAN11080   AC002443   AC093047   AE014134 AGB93167   AE014134 AGB93168   AY089584 AAL90322   BI170267   BI213008   BI214876   BI236256   BI236521   BI240985   BI362900   BI364510   BI632749   BI641172   BP547253   BQ103636   BT044074   CO279791   CO329777   D83701 BAA12067   EC232801   EC239384   EV582708   GH943546   GH947301   GH952931   GH959839   GH973171   GH976363   GH977700   L80118
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q0E8P0 Q24281 Q8SXK5
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism | ubiquitous   (Fisher et al., 2012) embryonic stage 7 -- 8   anterior endoderm anlage   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) posterior endoderm   (Fisher et al., 2012) embryonic stage 9 -- 10   anterior endoderm   (Fisher et al., 2012) germline cell   (Fisher et al., 2012) organism | faint & ubiquitous   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) posterior endoderm   (Fisher et al., 2012) embryonic stage 11 -- 12   anterior midgut primordium   (Fisher et al., 2012) germline cell   (Fisher et al., 2012) organism | faint & ubiquitous   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) posterior midgut primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic/larval midgut   (Fisher et al., 2012) gonad   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) northern blot Stage Tissue/Position (including subcellular localization) Reference adult stage & oogenesis   ovary   (Todo et al., 1996)
Additional Descriptive Data
	The 2 kb phr6-4 transcript is expressed at high levels in the adult ovary. (Todo et al., 1996)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
FlyAtlas Anatomical Expression Data (FlyAtlas-RNA.adult) (FlyAtlas-RNA.larva)    Styles Linear Logarithmic Heatmap Back-to-back    Scales gene max expression Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult testis. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (>999.999) Linear, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    53.675 Larval Midgut    14.8 Larval Hindgut    29 Larval Malpighian Tubules    9.7 Larval Fat Body    22.8 Larval Salivary Gland    18.2 Larval Trachea    28.675 Larval Carcass    24.125 Adult Head    8.5 Adult Eye    8.775 Adult Brain    13.6 Adult Thoracic-Abdominal Ganglion    23.1 Adult Crop    11.6 Adult Midgut    10 Adult Hindgut    9.9 Adult Malpighian Tubules    8.1 Adult Fat Body    20.9 Adult Salivary Gland    20.1 Adult Heart    12.2 Adult VirginFemale Spermatheca    16.4 Adult InseminatedFemale Spermatheca    15.9 Adult Ovary    68 Adult Testis    147.6 Adult Male Accessory Gland    14.4 Adult Carcass    21.3 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    8.5   NA  Eye    8.775   NA  Brain    no informative data   53.675  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    no informative data   NA  Crop    no informative data   no informative data  Midgut    no informative data   29  Hindgut    9.9   9.7  Malpighian Tubules    8.1   no informative data  Fat Body    no informative data   no informative data  Salivary Gland    no informative data   NA  Heart    no informative data   28.675  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    no informative data   NA  Ovary    68   NA  Testis    147.6   NA  Male Accessory Gland    no informative data   24.125  Carcass    no informative data FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
modENCODE Tissue Expression Data (modENCODE_mRNA-Seq_tissues)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Tissue   Expression Level imaginal disc, larvae L3 wandering    3 central nervous system, larvae L3    2 central nervous system, pupae P8    1 head, virgin 1-day female    0 head, virgin 4-day female    0 head, virgin 20-day female    0 head, mated 1-day female    0 head, mated 4-day female    0 head, mated 20-day female    0 head, mated 1-day male    0 head, mated 4-day male    1 head, mated 20-day male    1 salivary gland, larvae L3 wandering    0 salivary gland, white prepupae    0 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    1 digestive system, 4-day adult    1 digestive system, 20-day adult    1 fat body, larvae L3 wandering    0 fat body, white prepupae    1 fat body, pupae P8    1 carcass, larvae L3 wandering    2 carcass, 1-day adult    0 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    13 ovary, mated 4-day female    11 testis, mated 4-day male    4 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Tissue   Expression Level imaginal disc, larvae L3 wandering     central nervous system, larvae L3     central nervous system, pupae P8     head, virgin 1-day female     head, virgin 4-day female     head, virgin 20-day female     head, mated 1-day female     head, mated 4-day female     head, mated 20-day female     head, mated 1-day male     head, mated 4-day male     head, mated 20-day male     salivary gland, larvae L3 wandering     salivary gland, white prepupae     digestive system, larvae L3 wandering     digestive system, 1-day adult     digestive system, 4-day adult     digestive system, 20-day adult     fat body, larvae L3 wandering     fat body, white prepupae     fat body, pupae P8     carcass, larvae L3 wandering     carcass, 1-day adult     carcass, 4-day adult     carcass, 20-day adult     ovary, virgin 4-day female     ovary, mated 4-day female     testis, mated 4-day male     accessory gland, mated 4-day male
modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (modENCODE_mRNA-Seq_U)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic stages, in adult female stages. [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    37 embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day    28 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (37) embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day  (28) adult female 30day  (28) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    37 embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day    28 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    37 embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day    28 adult female 30day    28 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    37 embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day    28 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (37) embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day  28 adult female 30day  28 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    37 embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day    28 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    37 embryo 02-04hr    13 embryo 04-06hr    16 embryo 06-08hr    15 embryo 08-10hr    12 embryo 10-12hr    8 embryo 12-14hr    5 embryo 14-16hr    2 embryo 16-18hr    2 embryo 18-20hr    1 embryo 20-22hr    2 embryo 22-24hr    2 larva L1    2 larva L2    2 larva L3 12hr old    2 larva L3 puffstage 1-2    2 larva L3 puffstage 3-6    2 larva L3 puffstage 7-9    3 white prepupae new    3 white prepupae 12hr    4 white prepupae 24hr    3 pupae 2d postWPP    2 pupae 3d postWPP    1 pupae 4d postWPP    1 adult male 01day    1 adult male 05day    2 adult male 30day    2 adult female 01day    11 adult female 05day    28 adult female 30day    28 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
modENCODE Cell Line Expression Data (modENCODE_mRNA-Seq_cell.A) (modENCODE_mRNA-Seq_cell.B)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Cell Line   Expression Level Schneider line 2 S2R+    8 Schneider line 2 Sg4    14 embryonic 1182-4H    5 embryonic GM2    5 embryonic Kc167    16 embryonic S1    15 embryonic S3    4 leg disc CME L1    10 wing disc CME-W2    14 wing disc ML-DmD8    5 wing disc ML-DmD9    5 wing disc ML-DmD16-c3    5 wing disc ML-DmD21    7 wing disc ML-DmD32    3 haltere disc ML-DmD17-c3    6 eye-antennal disc ML-DmD11    1 antennal disc ML-DmD20-c5    6 mixed discs ML-DmD4-c1    6 CNS ML-DmBG1-c1    7 CNS ML-DmBG2-c2    12 tumorous blood cells mbn2    8 ovary fGS/OSS    1 ovary OSC    0 ovary OSS    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Cell Line   Expression Level Schneider line 2 S2R+     Schneider line 2 Sg4     embryonic 1182-4H     embryonic GM2     embryonic Kc167     embryonic S1     embryonic S3     leg disc CME L1     wing disc CME-W2     wing disc ML-DmD8     wing disc ML-DmD9     wing disc ML-DmD16-c3     wing disc ML-DmD21     wing disc ML-DmD32     haltere disc ML-DmD17-c3     eye-antennal disc ML-DmD11     antennal disc ML-DmD20-c5     mixed discs ML-DmD4-c1     CNS ML-DmBG1-c1     CNS ML-DmBG2-c2     tumorous blood cells mbn2     ovary fGS/OSS     ovary OSC     ovary OSS
modENCODE Treatments RNA-Seq
modENCODE Treatment Expression Data (modENCODE_mRNA-Seq_treatments)    Styles Linear Logarithmic Heatmap    Scales gene max expression Moderate expression bin max High expression bin max Extremely high expression bin max [download data (TSV)] Guide to modENCODE expression level colors   No/Extremely low expression (0 - 0)   Very low expression (1 - 3)   Low expression (4 - 10)   Moderate expression (11 - 25)   Moderately high expression (26 - 50)   High expression (51 - 100)   Very high expression (101 - 1000)   Extremely high expression (>1000) Linear, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Treatment   Expression Level extended cold, 4-day adult    1 cold shock, 4-day adult    1 heat shock, 4-day adult    4 Cadmium 50 mM 6 hrs, larvae L3    1 Cadmium 50 mM 12 hrs, larvae L3    1 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    6 Copper 0.5 mM 12 hrs, larvae L3    0 Copper 15 mM 48 hrs, 4-day adult    3 Zinc 5 mM 12 hrs, larvae L3    0 Zinc 4.5 mM 48 hrs, 4-day adult    1 Ethanol 2.5% 3 hrs, larvae L3    6 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    0 Caffeine 1.5 mg/ml 4 hrs, larvae L3    0 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    4 Caffeine 25 mg/ml 48 hrs, 4-day adult    2 Paraquat 5 mM 48 hrs, 4-day adult    4 Paraquat 10 mM 48 hrs, 4-day adult    6 Rotenone 2 μg 12 hrs, larvae L3    0 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Treatment   Expression Level extended cold, 4-day adult     cold shock, 4-day adult     heat shock, 4-day adult     Cadmium 50 mM 6 hrs, larvae L3     Cadmium 50 mM 12 hrs, larvae L3     Cadmium 50 mM 48 hrs, 4-day adult     Cadmium 100 mM 48 hrs, 4-day adult     Copper 0.5 mM 12 hrs, larvae L3     Copper 15 mM 48 hrs, 4-day adult     Zinc 5 mM 12 hrs, larvae L3     Zinc 4.5 mM 48 hrs, 4-day adult     Ethanol 2.5% 3 hrs, larvae L3     Ethanol 5% 3 hrs, larvae L3     Ethanol 10% 3 hrs, larvae L3     Caffeine 1.5 mg/ml 4 hrs, larvae L3     Caffeine 2.5 mg/ml 48 hrs, 4-day adult     Caffeine 25 mg/ml 48 hrs, 4-day adult     Paraquat 5 mM 48 hrs, 4-day adult     Paraquat 10 mM 48 hrs, 4-day adult     Rotenone 2 μg 12 hrs, larvae L3     Rotenone 8 μg 12 hrs, larvae L3
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_13 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	BDGP expression data • FI01404 RE11660 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0016054 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2488-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for phr6-4 Stages(s) 1-3 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable, with Scer\GAL4pnr-MD237 phr6-4GD4191 Phenotype manifest in Allele
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of phr6-4 Class Mutagen Stocks Known lesion phr6-4EY00214a 0 --
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of phr6-4 Class Mutagen Stocks Known lesion phr6-4GD4191 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes phr6-4GL01084 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes phr6-4KK107807 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes phr6-4NIG.2488R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2L)Exel7078 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4191} NA P{KK107807} NA P{NIG.2488R} NA P{TRiP.GL01084} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EPgy2}phr6-4EY00214a NA
Gene Ontology: Function, Process & Cellular Component ( 2 unique terms )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 2 terms )
Molecular Function
CV term Evidence References
DNA (6-4) photolyase activity inferred from sequence or structural similarity with EMBL:AB003687 (FlyBase, 1992-) non-traceable author statement (Todo, 1996.2.25)
Biological Process
CV term Evidence References
DNA repair inferred from sequence or structural similarity with EMBL:AB003687 (FlyBase, 1992-)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions phr6-4 allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0016054 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35322
Orthologs
OrthoDB Orthologs (42) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6P2QMX Dipteran inclusive ortholog search EOG6S7JZ7 Insect inclusive ortholog search EOG670SCV Arthropod inclusive ortholog search EOG6905RJ Metazoa inclusive ortholog search EOG6J4895
Orthologs in Drosophila Species (EOG6P2QMX)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\phr6-4     Drosophila simulans   Dsim\GD21692 Y   Drosophila sechellia   Dsec\GM23319 Y   Drosophila erecta   Dere\GG21562 Y   Drosophila yakuba   Dyak\GE12583 Y   Drosophila ananassae   Dana\GF14557 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA15376 Y   Drosophila persimilis   Dper\GL19603 Y   Drosophila willistoni   Dwil\GK15094 Y   Drosophila virilis   Dvir\GJ17431 Y   Drosophila mojavensis   Dmoj\GI19664 Y   Drosophila grimshawi   Dgri\GH10854 Y
Orthologs in non-Drosophila Dipterans (EOG6S7JZ7)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL001175   Anopheles gambiae Malaria mosquito  Agam\AGAP008651   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ017734
Orthologs in non-Dipteran Insects (EOG670SCV)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Acyrthosiphon pisum Pea aphid  Apim\ACYPI003810   Bombyx mori Silkmoth  Bmor\BGIBMGA000221
Orthologs in non-Insect Arthropods (EOG6905RJ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\Herpud2
Orthologs in non-Arthropod Metazoa (EOG6J4895)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_007204gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_000282gn Y Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_019722gn Y Danio rerio Zebrafish  Drer\cry1b Y Danio rerio Zebrafish  Drer\cry2a Y Danio rerio Zebrafish  Drer\cry4 Y Danio rerio Zebrafish  Drer\ENSDARG00000079444 Y Danio rerio Zebrafish  Drer\cry3 Y Danio rerio Zebrafish  Drer\cry5 Y Danio rerio Zebrafish  Drer\ENSDARG00000045768 Y Danio rerio Zebrafish  Drer\cry2b Y Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000003913 Y Xenopus tropicalis Western clawed frog  Xtro\cry2 Y Xenopus tropicalis Western clawed frog  Xtro\cry1 Y Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000015354 Y Gallus gallus Domestic chicken  Ggal\CRY1 Y Gallus gallus Domestic chicken  Ggal\LOC395100 Y Gallus gallus Domestic chicken  Ggal\CRY2 Y Mus musculus House mouse  Mmus\Cry2 Y Mus musculus House mouse  Mmus\Cry1 Y Rattus norvegicus Norway rat  Rnor\Cry1 Y Rattus norvegicus Norway rat  Rnor\Cry2 Y Homo sapiens Human  Hsap\ENSG00000121671 Y Homo sapiens Human  Hsap\CRY1 Y
Human Orthologs (2)
Gene OMIM HGNC Hsap\ENSG00000121671     Hsap\CRY1
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene 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
Stocks & Reagents
Stocks Listed in FlyBase ( 1 )
VDRC	v10461 w1118; P{GD4191}v10461
Genomic Clones ( 1 )
	BACR31P14 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	RE11660
Other clones	FI01404
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM03047 RE18308 RE21020 RE32289 RE32586 RE37954 RE47582 RE49645 SD24381 SD26613
Other clones	28183 191366 Dmel_dig_014146_0649_1524 EK136032 EK293835 FGH115A07 RP004136741 RP004210462 RP004249410 RP004282538 RP004321391 RP004386174 RP004552124 UUGC1045
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0016054 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35322
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity 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.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057840 NM_165334 NM_001273703 NM_001273704 RefSeq (Proteins) • NP_477188 NP_724274 NP_001260632 NP_001260633 DDBJ / EMBL / GenBank • AA695572 AAF53904 AAL90322 AAN11080 AC002443 AC093047 AGB93167 AGB93168 AY089584 BAA12067 BI170267 D83701 L80118 Entrez Gene - A searchable database of RefSeq genes. • 35322 UniProtKB/TrEMBL • Q0E8P0 Q8SXK5 Q24281
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • DNA photolyase, FAD-binding/Cryptochrome, C-terminal (IPR005101) DNA photolyase, N-terminal (IPR006050) Rossmann-like alpha/beta/alpha sandwich fold (IPR014729) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • FI01404 RE11660
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0016054 DRSC - Results from RNAi screens. • FBgn0016054 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0016054 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG2488-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0016054 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35322 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35322 modMine - Data generated by the modENCODE project. • FBgn0016054
Synonyms & Secondary IDs ( 12 )
Reported As
Symbol Synonym	38D.25 (McGill Drosophila Genome Project, 2001.9.25, Butler, 2001, Butler et al., 2001) 64PHR (Kanai et al., 1997) CG2488 (Ni et al., 2011.7.19, Keleman et al., 2009.8.5) D6-4 (Egan et al., 1999) Dm 64 (Todo, 1999) phr6-4 (Cox and Spradling, 2009, Japanese National Institute of Genetics, 2012.5.21) phr(6-4) (Zhao et al., 1997)
Name Synonym	6-4 photolyase (Okano et al., 1999, Yuan et al., 2007) (6-4)photolyase (Todo, 1999) (6-4)-photolyase (de Buendia, 1998, Zhao et al., 1997, Kim et al., 1994) (6-4) photolyase (Glas et al., 2009, Li et al., 2010, Maul et al., 2008) photolyase (Todo, 1996.2.25)
Secondary FlyBase IDs
References ( 39 )
Generate a list of	All references relating to this gene ( 39 )
List References by type	Research paper  ( 17 ) Supplementary material  ( 4 ) Review  ( 2 ) Personal communication to FlyBase  ( 7 ) FlyBase analysis  ( 3 ) DNA/RNA sequence record  ( 1 ) Stock list  ( 1 ) Curated genome annotation  ( 3 ) Website  ( 1 )
Recent research papers ( 1 )
	Selby and Sancar, 2012, Biochemistry 51(1): 167--171 The second chromophore in Drosophila photolyase/cryptochrome family photoreceptors. [FBrf0217122] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...