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Gene Dmel\Rif1

General Information
Symbol	Dmel\Rif1	Species	D. melanogaster
Name	Rap1 interacting factor 1 homolog	Annotation symbol	CG30085
Feature type	protein_coding_gene	FlyBase ID	FBgn0050085
Gene Model Status	Current	Stock availability	3 publicly available
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	52C8-52C8	Sequence location	2R:11,751,814..11,756,652 [-]
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 Rap1 interacting factor 1 homolog is referred to in FlyBase by the symbol Dmel\Rif1 (CG30085, FBgn0050085). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. The biological processes in which it is involved are not known. 4 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: Rap1-interacting factor 1 N-terminal. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, larval salivary gland, adult ovary. Comments on Affy2 ProbeSet: ProbeSet 1626755_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of CG30085. Gene sequence location is 2R:11751814..11756652.
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.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
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 52C8-52C8   Limits computationally determined from genome sequence between P{lacW}l(2)k05713k05713 and P{lacW}l(2)k02205k02205&P{PZ}sli05248
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Rif1 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Low-frequency RNA-Seq exon junction(s) not annotated. Gene model reviewed during 5.50
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Rif1-RA FBtr0087306  NM_166120   4605   1416
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Rif1-PA   FBpp0086441   156.8   1416   6.61     NP_725497   AAM70965
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Rap1-interacting factor 1 N-terminal (IPR022031)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA246489   AA438653   AA439905   AA440605   AA817112   AA817503   AA820255   AA951158   AA951272   AE013599 AAM70965   AF132192 AAD34780   AI455244   AI457000   AI511848   AI512695   AI515240   AI515399   AI515796   AI520025   AI531625   AI534552   AI544367   AI544370   BG636712   BG638028   BG639204   BG639577   BG640308   BI169503   BI243926   BI354531   BI363525   BI365328   BI365702   BI368549   BI369240   BI483438   BT022714   CO156729   CO266061   CO296754   CO300768   CO301815   CO336656   CO341942   DN154085   EC073934   EC074020   EC075415   EC198995   EC255272   EC261467   EV580320   GH822154   GH845336   GH847690   GH858249   GH869048   GH874262   GH907897   GH933613
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9XZ34
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   (Fisher et al., 2012) embryonic stage 7 -- 8   head mesoderm   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) embryonic stage 9 -- 10   antennal primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium central brain primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium visual primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium dorsal head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium lateral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium ventral head epidermis primordium   (Fisher et al., 2012) Comment:reported as procephalic ectoderm primordium anterior endoderm   (Fisher et al., 2012) inclusive hindgut primordium   (Fisher et al., 2012) organism | ubiquitous   (Fisher et al., 2012) trunk mesoderm   (Fisher et al., 2012) ventral ectoderm   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 11 -- 12   anterior midgut primordium   (Fisher et al., 2012) central brain primordium   (Fisher et al., 2012) hindgut proper primordium   (Fisher et al., 2012) Malpighian tubule primordium   (Fisher et al., 2012) posterior midgut primordium   (Fisher et al., 2012) salivary gland body primordium   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic hindgut   (Fisher et al., 2012) embryonic Malpighian tubule   (Fisher et al., 2012) embryonic/larval midgut   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nuclear heterochromatin inferred from direct assay (Sreesankar et al., 2012) nucleus inferred from direct assay (Sreesankar et al., 2012)
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: larval central nervous system, larval salivary gland, adult ovary. [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    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    125.675 Larval Midgut    24.7 Larval Hindgut    45.3 Larval Malpighian Tubules    4.4 Larval Fat Body    7.7 Larval Salivary Gland    157.2 Larval Trachea    59.175 Larval Carcass    65.625 Adult Head    27.6 Adult Eye    10.3 Adult Brain    24.3 Adult Thoracic-Abdominal Ganglion    22.5 Adult Crop    14.8 Adult Midgut    11.8 Adult Hindgut    15.9 Adult Malpighian Tubules    7.1 Adult Fat Body    15 Adult Salivary Gland    15.6 Adult Heart    5 Adult VirginFemale Spermatheca    15.1 Adult InseminatedFemale Spermatheca    9.8 Adult Ovary    468.7 Adult Testis    10.9 Adult Male Accessory Gland    4.9 Adult Carcass    24.1 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    27.6   NA  Eye    no informative data   NA  Brain    24.3   125.675  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    no informative data   NA  Crop    no informative data   no informative data  Midgut    no informative data   45.3  Hindgut    no informative data   4.4  Malpighian Tubules    7.1   7.7  Fat Body    no informative data   157.2  Salivary Gland    no informative data   NA  Heart    5   59.175  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    9.8   NA  Ovary    468.7   NA  Testis    no informative data   NA  Male Accessory Gland    4.9   65.625  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    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female    81 ovary, mated 4-day female    59 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female  (81) ovary, mated 4-day female  (59) testis, mated 4-day male    0 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    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female    81 ovary, mated 4-day female    59 testis, mated 4-day male    0 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    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female    81 ovary, mated 4-day female    59 testis, mated 4-day male    0 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    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female    81 ovary, mated 4-day female    59 testis, mated 4-day male    0 accessory gland, mated 4-day male    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female  (81) ovary, mated 4-day female  (59) testis, mated 4-day male    0 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    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female    81 ovary, mated 4-day female    59 testis, mated 4-day male    0 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    10 central nervous system, larvae L3    10 central nervous system, pupae P8    2 head, virgin 1-day female    1 head, virgin 4-day female    1 head, virgin 20-day female    1 head, mated 1-day female    2 head, mated 4-day female    0 head, mated 20-day female    1 head, mated 1-day male    1 head, mated 4-day male    1 head, mated 20-day male    2 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    2 digestive system, 20-day adult    2 fat body, larvae L3 wandering    0 fat body, white prepupae    2 fat body, pupae P8    1 carcass, larvae L3 wandering    6 carcass, 1-day adult    1 carcass, 4-day adult    3 carcass, 20-day adult    3 ovary, virgin 4-day female    81 ovary, mated 4-day female    59 testis, mated 4-day male    0 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 very high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic 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    115 embryo 02-04hr    134 embryo 04-06hr    97 embryo 06-08hr    67 embryo 08-10hr    52 embryo 10-12hr    28 embryo 12-14hr    23 embryo 14-16hr    27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day    37 adult female 30day    42 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (115) embryo 02-04hr  (134) embryo 04-06hr  (97) embryo 06-08hr  (67) embryo 08-10hr  (52) embryo 10-12hr  (28) embryo 12-14hr    23 embryo 14-16hr  (27) embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day  (37) adult female 30day  (42) Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr  (115) embryo 02-04hr  (134) embryo 04-06hr    97 embryo 06-08hr    67 embryo 08-10hr    52 embryo 10-12hr    28 embryo 12-14hr    23 embryo 14-16hr    27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day    37 adult female 30day    42 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    115 embryo 02-04hr    134 embryo 04-06hr    97 embryo 06-08hr    67 embryo 08-10hr    52 embryo 10-12hr    28 embryo 12-14hr    23 embryo 14-16hr    27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day    37 adult female 30day    42 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    115 embryo 02-04hr    134 embryo 04-06hr    97 embryo 06-08hr    67 embryo 08-10hr    52 embryo 10-12hr    28 embryo 12-14hr    23 embryo 14-16hr    27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day    37 adult female 30day    42 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (115) embryo 02-04hr  (134) embryo 04-06hr  (97) embryo 06-08hr  (67) embryo 08-10hr  (52) embryo 10-12hr  28 embryo 12-14hr    23 embryo 14-16hr  27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day  (37) adult female 30day  (42) Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr  115 embryo 02-04hr  134 embryo 04-06hr    97 embryo 06-08hr    67 embryo 08-10hr    52 embryo 10-12hr    28 embryo 12-14hr    23 embryo 14-16hr    27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day    37 adult female 30day    42 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    115 embryo 02-04hr    134 embryo 04-06hr    97 embryo 06-08hr    67 embryo 08-10hr    52 embryo 10-12hr    28 embryo 12-14hr    23 embryo 14-16hr    27 embryo 16-18hr    20 embryo 18-20hr    8 embryo 20-22hr    16 embryo 22-24hr    17 larva L1    9 larva L2    8 larva L3 12hr old    6 larva L3 puffstage 1-2    4 larva L3 puffstage 3-6    5 larva L3 puffstage 7-9    5 white prepupae new    4 white prepupae 12hr    9 white prepupae 24hr    5 pupae 2d postWPP    2 pupae 3d postWPP    2 pupae 4d postWPP    3 adult male 01day    1 adult male 05day    1 adult male 30day    1 adult female 01day    17 adult female 05day    37 adult female 30day    42 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+    71 Schneider line 2 Sg4    26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    33 wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2    34 ovary fGS/OSS    53 ovary OSC    20 ovary OSS    14 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (71) Schneider line 2 Sg4  26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3  (33) wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3  (30) eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1  26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2  (34) ovary fGS/OSS  (53) ovary OSC    20 ovary OSS    14 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    71 Schneider line 2 Sg4    26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    33 wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2    34 ovary fGS/OSS    53 ovary OSC    20 ovary OSS    14 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+    71 Schneider line 2 Sg4    26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    33 wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2    34 ovary fGS/OSS    53 ovary OSC    20 ovary OSS    14 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    71 Schneider line 2 Sg4    26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    33 wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2    34 ovary fGS/OSS    53 ovary OSC    20 ovary OSS    14 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+  (71) Schneider line 2 Sg4  26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3  (33) wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3  30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1  26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2  (34) ovary fGS/OSS  (53) ovary OSC    20 ovary OSS    14 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    71 Schneider line 2 Sg4    26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    33 wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2    34 ovary fGS/OSS    53 ovary OSC    20 ovary OSS    14 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+    71 Schneider line 2 Sg4    26 embryonic 1182-4H    17 embryonic GM2    16 embryonic Kc167    14 embryonic S1    18 embryonic S3    23 leg disc CME L1    22 wing disc CME-W2    14 wing disc ML-DmD8    19 wing disc ML-DmD9    17 wing disc ML-DmD16-c3    33 wing disc ML-DmD21    19 wing disc ML-DmD32    15 haltere disc ML-DmD17-c3    30 eye-antennal disc ML-DmD11    18 antennal disc ML-DmD20-c5    23 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    26 CNS ML-DmBG2-c2    16 tumorous blood cells mbn2    34 ovary fGS/OSS    53 ovary OSC    20 ovary OSS    14 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    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult    48 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    47 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult    28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult  (48) Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3  (47) Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (39) Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult  (28) Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult    48 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    47 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult    28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 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    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult    48 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    47 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult    28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 Expression Level Scale  Extremely high  log, scaled to maximum expression level Treatment   Expression Level extended cold, 4-day adult    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult    48 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    47 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult    28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult  (48) Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3  (47) Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult  (39) Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult  28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Treatment   Expression Level extended cold, 4-day adult    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult    48 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    47 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult    28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 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    8 cold shock, 4-day adult    4 heat shock, 4-day adult    16 Cadmium 50 mM 6 hrs, larvae L3    4 Cadmium 50 mM 12 hrs, larvae L3    2 Cadmium 50 mM 48 hrs, 4-day adult    21 Cadmium 100 mM 48 hrs, 4-day adult    48 Copper 0.5 mM 12 hrs, larvae L3    1 Copper 15 mM 48 hrs, 4-day adult    14 Zinc 5 mM 12 hrs, larvae L3    1 Zinc 4.5 mM 48 hrs, 4-day adult    6 Ethanol 2.5% 3 hrs, larvae L3    47 Ethanol 5% 3 hrs, larvae L3    2 Ethanol 10% 3 hrs, larvae L3    3 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    39 Caffeine 25 mg/ml 48 hrs, 4-day adult    10 Paraquat 5 mM 48 hrs, 4-day adult    28 Paraquat 10 mM 48 hrs, 4-day adult    25 Rotenone 2 μg 12 hrs, larvae L3    3 Rotenone 8 μg 12 hrs, larvae L3    5 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_08 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	BDGP expression data • LD22218 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0050085 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG30085-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Rif1 Stages(s) 1-3 Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable, with Scer\GAL4pnr-MD237 Rif1GD9990 Phenotype manifest in Allele
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of Rif1 Class Mutagen Stocks Known lesion Rif1G18022 P-element activity 1 --
Alleles Carried on Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Rif1 Class Mutagen Stocks Known lesion Rif1GD9990 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Rif1KK100633 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes Rif1NIG.30085R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}Rif1G18022 NA
Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
	There is no information supporting a biological process term for this gene. (Based on a review of available data before: 2006)
Terms Based on Experimental Evidence ( 4 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
NOT maintenance of chromatin silencing at telomere inferred from mutant phenotype (Sreesankar et al., 2012) NOT response to DNA damage stimulus inferred from direct assay (Sreesankar et al., 2012) inferred from mutant phenotype (Sreesankar et al., 2012)
Cellular Component
CV term Evidence References
nuclear heterochromatin inferred from direct assay (Sreesankar et al., 2012) nucleus inferred from direct assay (Sreesankar et al., 2012)
Terms Based on Predictions or Assertions ( 0 terms )
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Rif1 - Cyp6a22 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Rif1 - Pp1-87B anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Rif1 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 73027 DroID - A comprehensive database of gene and protein interactions. • FBgn0050085 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 246445
Orthologs
OrthoDB Orthologs (45) - 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 EOG60P4S2 Dipteran inclusive ortholog search EOG6DBTNM Insect inclusive ortholog search EOG6GQP0W Arthropod inclusive ortholog search EOG61NS1Z Metazoa inclusive ortholog search EOG6SJJ7T
Orthologs in Drosophila Species (EOG60P4S2)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\Rif1     Drosophila simulans   Dsim\GD25592 Y   Drosophila sechellia   Dsec\GM20115 Y   Drosophila erecta   Dere\GG22327 Y   Drosophila yakuba   Dyak\GE14124 Y   Drosophila ananassae   Dana\GF13365 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA15636 Y   Drosophila persimilis   Dper\GL16842 Y   Drosophila willistoni   Dwil\GK20795 Y   Drosophila virilis   Dvir\GJ22233 Y   Drosophila mojavensis   Dmoj\GI19102 Y   Drosophila grimshawi   Dgri\GH21278 Y
Orthologs in non-Drosophila Dipterans (EOG6DBTNM)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL001322   Anopheles gambiae Malaria mosquito  Agam\AGAP010393   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ020224
Orthologs in non-Dipteran Insects (EOG6GQP0W)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB43771   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG015584   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG015585   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH21592   Atta cephalotes Leafcutter ant  Acep\ACEP15307   Camponotus floridanus Florida carpenter ant  Cflo\CFLO14453   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL13666   Linepithema humile Argentine ant  Lhum\LH16569   Pogonomyrmex barbatus Red harvester ant  Pbar\PB12799   Solenopsis invicta Red fire ant  Sinv\SINV15886   Acyrthosiphon pisum Pea aphid  Apim\ACYPI37402   Bombyx mori Silkmoth  Bmor\BGIBMGA006763   Tribolium castaneum Red flour beetle  Tcas\TC001961   Tribolium castaneum Red flour beetle  Tcas\TC012353
Orthologs in non-Insect Arthropods (EOG61NS1Z)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\nad7   Ixodes scapularis Deer tick  Isca\ISCW021260
Orthologs in non-Arthropod Metazoa (EOG6SJJ7T)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\F11E6.7   Caenorhabditis elegans Nematode  Cele\F19H6.3   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_019463gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_025047gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_011055gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_012553gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_006009gn   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_023093gn   Danio rerio Zebrafish  Drer\rif1   Xenopus tropicalis Western clawed frog  Xtro\rif1   Gallus gallus Domestic chicken  Ggal\RIF1   Mus musculus House mouse  Mmus\Rif1   Rattus norvegicus Norway rat  Rnor\Rif1   Homo sapiens Human  Hsap\RIF1
Human Orthologs (1)
Gene OMIM HGNC Hsap\RIF1
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD25592 Drosophila sechellia Dsec\GM20115 Drosophila erecta Dere\GG22327 Drosophila yakuba Dyak\GE14124 Drosophila ananassae Dana\GF13365 Drosophila pseudoobscura pseudoobscura Dpse\GA15636 Drosophila persimilis Dper\GL16842 Drosophila willistoni Dwil\GK20795 Drosophila virilis Dvir\GJ22233 Drosophila mojavensis Dmoj\GI19102 Drosophila grimshawi Dgri\GH21278
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Bloomington	27427 y1 w*; P{EP}Rif1G18022
VDRC	v33673 w1118 P{GD9990}v33673 v33672 w1118; P{GD9990}v33672
Genomic Clones ( 2 )
	BACR04J01 BACR07M03 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 53 )
	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	LD22218 RE66338
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM27204 LD05266 LD14591 LD15438 LD23143 LD23774 LD31655 LD37204 LD39952 LD41467 LD43386 LD44647 LD47213 RE10690 RE41744 RE48355 RE50596 RE51069 RE54538 RE55361 SD07444 SD10904 SD10907 SD11292 SD14480
Other clones	34565 54133 55388 76702 214441.75 558092 Dmel_dig_009382_0589_2648 EK144826 EK174738 EK179355 EK182230 EK215106 EN09008 EN12955 EP13459 LD12971 LD46979 RP003122635 RP003131691 RP003241327 RP003254026 RP003318957 RP003512732 RP003612159 RP003650178 SD02776
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0050085 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 246445
Antibody Information
	polyclonal (Sreesankar et al., 2012)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Rif1 CG30085 (Sreesankar et al., 2012)
Source for database merge of
Additional comments
Other Comments
	New annotation (CG30085) in release 3 of the genome annotation. (FlyBase Genome Annotators, 2002-2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_166120 RefSeq (Proteins) • NP_725497 DDBJ / EMBL / GenBank • AA817112 AAD34780 AAM70965 AF132192 AI455244 BI483438 Entrez Gene - A searchable database of RefSeq genes. • 246445 UniProtKB/TrEMBL • Q9XZ34
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Rap1-interacting factor 1 N-terminal (IPR022031) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • LD22218
Linkouts
	BioGRID - A database of protein and genetic interactions • 73027 DroID - A comprehensive database of gene and protein interactions. • FBgn0050085 DRSC - Results from RNAi screens. • FBgn0050085 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0050085 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG30085-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0050085 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 246445 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 246445 modMine - Data generated by the modENCODE project. • FBgn0050085
Synonyms & Secondary IDs ( 5 )
Reported As
Symbol Synonym	BcDNA:LD22218   CG30085 (Sreesankar et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Ayroles et al., 2009, Keleman et al., 2009.8.5) dRif1 (Sreesankar et al., 2012) Rif1
Name Synonym	Rap1 interacting factor 1 homolog
Secondary FlyBase IDs
	FBgn0027510
References ( 18 )
Research paper	Sreesankar et al., 2012, BMC Genomics 13: 255 Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes. [FBrf0219090] Blanco et al., 2010, BMC Dev. Biol. 10: 94 Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs. [FBrf0211812] Ayroles et al., 2009, Nat. Genet. 41(3): 299--307 Systems genetics of complex traits in Drosophila melanogaster. [FBrf0206705]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 33. Fuzzy Cluster Members. [FBrf0213980] The modENCODE Consortium, 2010, Science 330(6012): DataS14: Gene co-expression clusters. [FBrf0213979] Mummery-Widmer et al., 2009, Nature 458(7241): Supplementary Table 2 - Genome-wide bristle screen results. [FBrf0214518] Giot et al., 2003, Science 302(5651): Tables S1 to S7. [FBrf0166452]
Personal communication to FlyBase	Bellen, 2009.5.5, BDGP_2009_0507.GenExel.xml BDGP_2009_0507.GenExel.xml [FBrf0207859] Keleman et al., 2009.8.5, RNAi-phiC31 construct and insertion data submitted by the Vienna Drosophila RNAi Center RNAi-phiC31 construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0208510] Mintseris et al., 2009.11.23, DPiM: the Drosophila Protein Interaction Mapping project DPiM: the Drosophila Protein Interaction Mapping project [FBrf0209452] Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327] FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215] BDGP Project Members, 2000-, Berkeley Drosophila Genome Project. (Computer file) Berkeley Drosophila Genome Project. (Computer file) [FBrf0125078] Misra, 2000.4.8, Annotation identities: Category 5. Annotation identities: Category 5. [FBrf0126712]
FlyBase analysis	FlyBase Genome Annotators, 2002-2003, Changes affecting gene model number or type in releases 3.0 and 3.1 of the annotated D.melanogaster genome. Changes affecting gene model number or type in releases 3.0 and 3.1 of the annotated D.melanogaster genome. [FBrf0148886] FlyBase Curators, 2002-, Use of the ND evidence code for Gene Ontology (GO) terms in FlyBase. Use of the ND evidence code for Gene Ontology (GO) terms in FlyBase. [FBrf0159398]
Stock list	Japanese National Institute of Genetics, 2012.5.21, RNAi stocks available from NIG-FLY. RNAi stocks available from NIG-FLY. [FBrf0218457]
Website	Fisher et al., 2012, BDGP insitu homepage BDGP insitu homepage [FBrf0219073]