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Gene Dmel\SoxN

General Information
Symbol	Dmel\SoxN	Species	D. melanogaster
Name	SoxNeuro	Annotation symbol	CG18024
Feature type	protein_coding_gene	FlyBase ID	FBgn0029123
Gene Model Status	Current	Stock availability	4 publicly available
Also Known As	DM64
Genomic Location
Chromosome (arm)	2L	Recombination map
Cytogenetic map	29F2-29F2	Sequence location	2L:8,825,645..8,829,670 [+]
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 SoxNeuro is referred to in FlyBase by the symbol Dmel\SoxN (CG18024, FBgn0029123). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: chromatin DNA binding; protein binding; RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity. There is experimental evidence that it is involved in the biological process: central nervous system development; regulation of Wnt receptor signaling pathway; positive regulation of transcription from RNA polymerase II promoter; axon guidance; nervous system development. 17 alleles are reported. The phenotypes of these alleles are annotated with: ventral nerve cord primordium; portion of tissue; organ system; extended germ band embryo; organ system subdivision; embryonic/larval neuron; acellular anatomical structure; adult segment; multicellular structure; stage 2 neuroblast. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: High mobility group (HMG) box domain. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed within 00-12 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: larval/adult central nervous system. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, adult thoracico-abdominal ganglion, larval salivary gland. Comments on Affy2 ProbeSet: ProbeSet 1631408_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of SoxN. Gene sequence location is 2L:8825645..8829670.
User Contributed Data
	Beta version, feedback welcome
External Summaries
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 29F2-29F2   Limits computationally determined from genome sequence between P{lacW}l(2)k04003k04003 and P{PZ}tai01351
Experimentally Determined Cytological Location
Cytogenetic map Notes References 29F1-29F2     (Girad, 1999.12.21)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\SoxN 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 5.44 Gene model reviewed during 5.50 gene_with_stop_codon_read_through ; SO:0000697 Stop-codon suppression (UGA) postulated; FBrf0216885.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) SoxN-RA FBtr0079733  NM_079996   4026   572 SoxN-RB FBtr0330210  NM_001273340   4026   761
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 SoxN-PA   FBpp0079335   61.8   572   9.78     NP_524735   AAF52712 SoxN-PB   FBpp0303243   81.6   761   9.31     NP_001260269   AGB92805
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • High mobility group (HMG) box domain (IPR009071)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014134 AAF52712   AE014134 AGB92805   AI512383   AJ252124 CAB64386   AW943710   BI240511   BI563971   BI588714   BI611307   BI611825   BI630477   BI631498   BT001514 AAN71269   CK135040   CO189520   CO263477   CO264539   CO274553   CO275698   CO277916   CO282836   CO297145   CO299490   CO300574   CO301140   CO304926   CO342253   EC060686   EC072360   EC074195   EC080602   EC082227   EC085650   EC197180   EC198148   EC199238   EC201864   EC205945   EC212490   EC214562   EC219691   EC221435   EC232944   EC241181   EC245485   EC245563   EC249035   EC257842   ES693555   ES693558   M86334 AAA28475
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VLH8 Q9U1H5
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 regulatory region FBsf0000435248 2L:8,811,796..8,812,360 evidence=Reporter construct (in vivo) (Zhai et al., 2011, Halfon, 2012.6.19) regulatory region FBsf0000436264 2L:8,841,420..8,842,089 evidence=Reporter construct (in vivo) (Junion et al., 2012, Halfon, 2012.6.19)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 3   embryonic head | precursor   (Cremazy et al., 2000) embryonic stage 4 -- 6   central brain anlage in statu nascendi   (Fisher et al., 2012) ventral ectoderm anlage   (Fisher et al., 2012) Comment:anlage in statu nascendi antennal anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi dorsal head epidermis anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi visual anlage in statu nascendi   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage in statu nascendi embryonic stage 4 -- 7   procephalic neurogenic region   (Cremazy et al., 2000) lateral ventral neurectoderm   (Cremazy et al., 2000) Comment:excluded from ventral midline embryonic stage 7 -- 8   antennal anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage central brain anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage dorsal head epidermis anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage visual anlage   (Fisher et al., 2012) Comment:reported as procephalic ectoderm anlage ventral ectoderm   (Fisher et al., 2012) embryonic stage 8   ventral nerve cord primordium   (Buescher et al., 2002) Comment:NOT ventral midline embryonic/larval central nervous system   (Cremazy et al., 2000) embryonic stage 9   embryonic/larval central nervous system | segmentally repeated   (Cremazy et al., 2000) 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 ventral ectoderm   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 10   ventral neurectoderm   (Buescher et al., 2002) Comment:NOT neuroblast embryonic neuroblast | subset   (Cremazy et al., 2000) embryonic stage 11 -- 12   central brain primordium   (Fisher et al., 2012) embryonic central brain glial cell   (Fisher et al., 2012) embryonic central brain neuron   (Fisher et al., 2012) lateral cord glial cell   (Fisher et al., 2012) lateral cord neuron   (Fisher et al., 2012) ventral epidermis primordium   (Fisher et al., 2012) ventral nerve cord primordium   (Fisher et al., 2012) embryonic stage 12   ventral nerve cord primordium & presumptive embryonic/larval central nervous system | restricted   (Buescher et al., 2002) Comment:stripe of expression in the ventral nerve cord primordium embryonic stage 13 -- 16   embryonic brain   (Fisher et al., 2012) embryonic ventral epidermis   (Fisher et al., 2012) ventral nerve cord   (Fisher et al., 2012) embryonic stage 17   chordotonal organ   (Cremazy et al., 2000) epidermis | ventro-lateral   (Cremazy et al., 2000) embryonic/larval brain   (Cremazy et al., 2000)
Additional Descriptive Data
	Expression of transcript is observed throughout the developing neuroectoderm. Expression is lost in delaminated neuroblasts. While transcript is ubiquitous in the neuroectoderm it is not uniform. In stage 12 embryos transcript can be detected in some cells of the central and peripheral nervous system. (Buescher et al., 2002)
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4 -- 7   lateral ventral neurectoderm   • nucleus (Cremazy et al., 2000) embryonic stage 8   ventral neurectoderm   (Buescher et al., 2002) Comment:NOT ventral midline embryonic stage 10   ventral nerve cord primordium   (Buescher et al., 2002) Comment:NOT neuroblast embryonic stage 12   ventral nerve cord primordium | restricted & central nervous system | restricted   (Buescher et al., 2002) Comment:stripe of expression in ventral nerve cord primordium embryonic stage 17   chordotonal organ   • nucleus (Cremazy et al., 2000) epidermis | ventro-lateral   • nucleus (Cremazy et al., 2000) third instar larval stage   eye disc posterior to the morphogenetic furrow   • nucleus (Cremazy et al., 2001) antennal disc | restricted   • nucleus (Cremazy et al., 2001) second segment of antenna | precursor   • nucleus (Cremazy et al., 2001) third segment of antenna | precursor   • nucleus (Cremazy et al., 2001) ventral thoracic disc | restricted   • nucleus (Cremazy et al., 2001) neuroblast of embryonic/larval optic lobe   • nucleus (Cremazy et al., 2001) larval inner optic anlage   • nucleus (Cremazy et al., 2001) larval outer optic anlage   • nucleus (Cremazy et al., 2001) abdominal neuroblast   • nucleus (Cremazy et al., 2001) thoracic neuroblast   • nucleus (Cremazy et al., 2001) inferred from author statements Stage Tissue/Position (including subcellular localization) Reference third instar larval stage   embryonic/larval salivary gland   • nucleus (Cremazy et al., 2001)
Additional Descriptive Data
	furrow. In the leg discs, SoxN is expressed in a few cells in the center of the disc, and in two lateral patches in the dorsal/posterior and ventral/anterior quadrants. SoxN is also expressed in neuroblasts of the optic proliferation centers and central brain, and in thoracic and abdominal neuroblasts. (Cremazy et al., 2001) In the third instar larval antennal disc, SoxN is expressed in three stripes of cells in the part of the disc that will give rise to the to antennal segments 2 and 3. In the eye disc, SoxN is expressed in differentiated photoreceptor cells posterior to the morphogenetic (Cremazy et al., 2001) SoxN proteinexpression largely overlaps the transcript expression in stage 8-10 developing embryos, with expression in the neuroectoderm and absent or strongly reduced in delaminating neuroblasts. (Buescher et al., 2002)
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
nucleus inferred from direct assay (Savare et al., 2005)
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 high levels in the following post-embryonic organs or tissues: larval/adult central nervous system. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, adult thoracico-abdominal ganglion, larval salivary gland. [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    936.25 Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain    790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System  (936.25) Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain  (790.8) Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    936.25 Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain    790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    936.25 Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain    790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  Very high  log, scaled to maximum expression level Tissue   Expression Level Larval Central Nervous System    936.25 Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain    790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System  (936.25) Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain  790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    936.25 Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain    790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    936.25 Larval Midgut    4.8 Larval Hindgut    7.8 Larval Malpighian Tubules    4.9 Larval Fat Body    23.3 Larval Salivary Gland    304.6 Larval Trachea    49.8 Larval Carcass    58.25 Adult Head    169.2 Adult Eye    194.475 Adult Brain    790.8 Adult Thoracic-Abdominal Ganglion    206 Adult Crop    7.4 Adult Midgut    1.1 Adult Hindgut    4.9 Adult Malpighian Tubules    2.9 Adult Fat Body    22.1 Adult Salivary Gland    69.9 Adult Heart    5.25 Adult VirginFemale Spermatheca    29.9 Adult InseminatedFemale Spermatheca    31 Adult Ovary    0.6 Adult Testis    3.9 Adult Male Accessory Gland    10.1 Adult Carcass    10.6 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    169.2   NA  Eye    194.475   NA  Brain    790.8   936.25  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    206   NA  Crop    7.4   4.8  Midgut    1.1   7.8  Hindgut    4.9   4.9  Malpighian Tubules    2.9   no informative data  Fat Body    22.1   304.6  Salivary Gland    69.9   NA  Heart    5.25   49.8  Trachea    NA   NA  VirginFemale Spermatheca    29.9   NA  InseminatedFemale Spermatheca    31   NA  Ovary    0.6   NA  Testis    3.9   NA  Male Accessory Gland    no informative data   58.25  Carcass    10.6 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    13 central nervous system, larvae L3    100 central nervous system, pupae P8    37 head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering    31 salivary gland, white prepupae    447 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3  (100) central nervous system, pupae P8  (37) head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering  (31) salivary gland, white prepupae  (447) digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    100 central nervous system, pupae P8    37 head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering    31 salivary gland, white prepupae  (447) digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 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    13 central nervous system, larvae L3    100 central nervous system, pupae P8    37 head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering    31 salivary gland, white prepupae    447 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 Expression Level Scale  Extremely high  log, scaled to maximum expression level Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    100 central nervous system, pupae P8    37 head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering    31 salivary gland, white prepupae    447 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 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    13 central nervous system, larvae L3  (100) central nervous system, pupae P8  (37) head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering  31 salivary gland, white prepupae  (447) digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Tissue   Expression Level imaginal disc, larvae L3 wandering    13 central nervous system, larvae L3    100 central nervous system, pupae P8    37 head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering    31 salivary gland, white prepupae  (447) digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 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    13 central nervous system, larvae L3    100 central nervous system, pupae P8    37 head, virgin 1-day female    13 head, virgin 4-day female    17 head, virgin 20-day female    7 head, mated 1-day female    14 head, mated 4-day female    13 head, mated 20-day female    9 head, mated 1-day male    24 head, mated 4-day male    25 head, mated 20-day male    19 salivary gland, larvae L3 wandering    31 salivary gland, white prepupae    447 digestive system, larvae L3 wandering    1 digestive system, 1-day adult    0 digestive system, 4-day adult    0 digestive system, 20-day adult    0 fat body, larvae L3 wandering    0 fat body, white prepupae    9 fat body, pupae P8    14 carcass, larvae L3 wandering    15 carcass, 1-day adult    1 carcass, 4-day adult    1 carcass, 20-day adult    1 ovary, virgin 4-day female    0 ovary, mated 4-day female    0 testis, mated 4-day male    0 accessory gland, mated 4-day male    4 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 high expression to a trough of very low expression. Peak expression observed within 00-12 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    3 embryo 02-04hr    67 embryo 04-06hr    86 embryo 06-08hr    59 embryo 08-10hr    40 embryo 10-12hr    24 embryo 12-14hr    27 embryo 14-16hr    29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    28 white prepupae new    36 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr  (67) embryo 04-06hr  (86) embryo 06-08hr  (59) embryo 08-10hr  (40) embryo 10-12hr    24 embryo 12-14hr  (27) embryo 14-16hr  (29) embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9  (28) white prepupae new  (36) white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    67 embryo 04-06hr    86 embryo 06-08hr    59 embryo 08-10hr    40 embryo 10-12hr    24 embryo 12-14hr    27 embryo 14-16hr    29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    28 white prepupae new    36 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 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    3 embryo 02-04hr    67 embryo 04-06hr    86 embryo 06-08hr    59 embryo 08-10hr    40 embryo 10-12hr    24 embryo 12-14hr    27 embryo 14-16hr    29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    28 white prepupae new    36 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Extremely high  log, scaled to maximum expression level Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    67 embryo 04-06hr    86 embryo 06-08hr    59 embryo 08-10hr    40 embryo 10-12hr    24 embryo 12-14hr    27 embryo 14-16hr    29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    28 white prepupae new    36 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr  (67) embryo 04-06hr  (86) embryo 06-08hr  (59) embryo 08-10hr  (40) embryo 10-12hr    24 embryo 12-14hr  27 embryo 14-16hr  29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9  28 white prepupae new  (36) white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    67 embryo 04-06hr    86 embryo 06-08hr    59 embryo 08-10hr    40 embryo 10-12hr    24 embryo 12-14hr    27 embryo 14-16hr    29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    28 white prepupae new    36 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 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    3 embryo 02-04hr    67 embryo 04-06hr    86 embryo 06-08hr    59 embryo 08-10hr    40 embryo 10-12hr    24 embryo 12-14hr    27 embryo 14-16hr    29 embryo 16-18hr    20 embryo 18-20hr    21 embryo 20-22hr    11 embryo 22-24hr    10 larva L1    10 larva L2    7 larva L3 12hr old    4 larva L3 puffstage 1-2    3 larva L3 puffstage 3-6    9 larva L3 puffstage 7-9    28 white prepupae new    36 white prepupae 12hr    14 white prepupae 24hr    14 pupae 2d postWPP    8 pupae 3d postWPP    5 pupae 4d postWPP    5 adult male 01day    4 adult male 05day    4 adult male 30day    4 adult female 01day    2 adult female 05day    1 adult female 30day    1 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+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate  Linear, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 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+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Extremely high  log, scaled to maximum expression level Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to Moderate expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 Expression Level Scale  Very low   Low   Moderate   Moderately high  log, scaled to High expression Cell Line   Expression Level Schneider line 2 S2R+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 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+    0 Schneider line 2 Sg4    0 embryonic 1182-4H    0 embryonic GM2    0 embryonic Kc167    2 embryonic S1    0 embryonic S3    0 leg disc CME L1    0 wing disc CME-W2    0 wing disc ML-DmD8    0 wing disc ML-DmD9    0 wing disc ML-DmD16-c3    0 wing disc ML-DmD21    0 wing disc ML-DmD32    0 haltere disc ML-DmD17-c3    1 eye-antennal disc ML-DmD11    0 antennal disc ML-DmD20-c5    0 mixed discs ML-DmD4-c1    19 CNS ML-DmBG1-c1    0 CNS ML-DmBG2-c2    0 tumorous blood cells mbn2    0 ovary fGS/OSS    0 ovary OSC    0 ovary OSS    0 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    85 cold shock, 4-day adult    62 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3    35 Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    37 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High  Linear, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult  (85) cold shock, 4-day adult  (62) heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3  (35) Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult  (37) Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 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    85 cold shock, 4-day adult    62 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3    35 Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    37 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 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    85 cold shock, 4-day adult    62 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3    35 Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    37 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 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    85 cold shock, 4-day adult    62 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3    35 Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    37 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 Rotenone 8 μg 12 hrs, larvae L3    1 Expression Level Scale  Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Moderate expression Treatment   Expression Level extended cold, 4-day adult  (85) cold shock, 4-day adult  (62) heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3  (35) Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult  (37) Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 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    85 cold shock, 4-day adult    62 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3    35 Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    37 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 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    85 cold shock, 4-day adult    62 heat shock, 4-day adult    1 Cadmium 50 mM 6 hrs, larvae L3    2 Cadmium 50 mM 12 hrs, larvae L3    5 Cadmium 50 mM 48 hrs, 4-day adult    3 Cadmium 100 mM 48 hrs, 4-day adult    2 Copper 0.5 mM 12 hrs, larvae L3    8 Copper 15 mM 48 hrs, 4-day adult    4 Zinc 5 mM 12 hrs, larvae L3    35 Zinc 4.5 mM 48 hrs, 4-day adult    9 Ethanol 2.5% 3 hrs, larvae L3    1 Ethanol 5% 3 hrs, larvae L3    1 Ethanol 10% 3 hrs, larvae L3    2 Caffeine 1.5 mg/ml 4 hrs, larvae L3    2 Caffeine 2.5 mg/ml 48 hrs, 4-day adult    1 Caffeine 25 mg/ml 48 hrs, 4-day adult    37 Paraquat 5 mM 48 hrs, 4-day adult    2 Paraquat 10 mM 48 hrs, 4-day adult    2 Rotenone 2 μg 12 hrs, larvae L3    2 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_11 mE1_20_mRNA_expression_cluster_04
External Data & Images
Linkouts	BDGP expression data • LD44245 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0029123 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG18024-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for SoxN Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal, with Scer\GAL4pnr-MD237 SoxNGD4415 lethal | embryonic stage SoxNNC14 lethal | embryonic stage, with Scer\GAL4da.G32 SoxNK439.Scer\UAS lethal | embryonic stage, with Scer\GAL4e22c SoxNScer\UAS.cOa lethal | embryonic stage (with Df(2L)Exel7040) SoxNNC14 lethal | larval stage, with Scer\GAL4unspecified SoxNK439.Scer\UAS partially lethal - majority die | embryonic stage, with Scer\GAL4arm.PS SoxNScer\UAS.cOa partially lethal - majority die | pupal stage, with Scer\GAL4dpp.blk1 SoxNScer\UAS.cOa Other Phenotypes Allele neuroanatomy defective SoxNdsRNA.cIa SoxNGA1192 SoxNU6-35 SoxNunspecified neuroanatomy defective | embryonic stage SoxNGA1192 neuroanatomy defective | embryonic stage, with Scer\GAL4da.G32 SoxNK439.Scer\UAS neuroanatomy defective | embryonic stage, with Scer\GAL4elav.PLu SoxNK439.Scer\UAS Phenotype manifest in Allele aCC neuron SoxNGA1192 adult head, with Scer\GAL4ey.PB SoxNK439.Scer\UAS anterior commissure SoxNGA1192 anterior commissure, with Scer\GAL4da.G32 SoxNK439.Scer\UAS anterior commissure, with Scer\GAL4elav.PLu SoxNK439.Scer\UAS axon & ventral nerve cord SoxNGA1192 axon & ventral nerve cord, with Scer\GAL4elav.PLu SoxNK439.Scer\UAS commissure SoxNU6-35 SoxNunspecified connective SoxNunspecified denticle SoxNGA1192 SoxNU6-35 denticle | cell autonomous | ectopic, with Scer\GAL4wg.PM SoxNScer\UAS.T:Avic\GFP-YFP.Venus denticle | ectopic, with Scer\GAL4arm.T:Hsim\VP16 SoxNScer\UAS.T:Avic\GFP-YFP.Venus denticle | ectopic, with Scer\GAL4en-e16E SoxNScer\UAS.cOa denticle belt SoxNGA1192 SoxNNC14 denticle belt, with Df(3R)Espl22, Scer\GAL4e22c SoxNScer\UAS.cOa denticle belt, with Scer\GAL4e22c SoxNScer\UAS.cOa denticle belt (with Df(2L)Exel7040) SoxNNC14 denticle row | ectopic, with Scer\GAL4e22c SoxNScer\UAS.cOa EG neuron SoxNU6-35 EL neuron SoxNGA1192 SoxNU6-35 embryonic/first instar larval cuticle SoxNGA1192 SoxNNC14 embryonic/first instar larval cuticle, with Df(3R)Espl22, Scer\GAL4e22c SoxNScer\UAS.cOa embryonic/first instar larval cuticle, with Scer\GAL4e22c SoxNScer\UAS.cOa embryonic/first instar larval cuticle (with Df(2L)Exel7040) SoxNNC14 embryonic/larval glial cell SoxNU6-35 embryonic/larval neuron SoxNU6-35 embryonic head SoxNGA1192 embryonic neuroblast SoxNU6-35 extended germ band embryo SoxNU6-35 eye, with Scer\GAL4ey.PB SoxNScer\UAS.cBa ganglion mother cell SoxNGA1192 leg, with Scer\GAL4unspecified SoxNScer\UAS.cBa longitudinal connective SoxNU6-35 longitudinal connective, with Scer\GAL4da.G32 SoxNK439.Scer\UAS longitudinal connective, with Scer\GAL4elav.PLu SoxNK439.Scer\UAS midgut constriction SoxNGA1192 neuroblast MP2 SoxNGA1192 SoxNU6-35 neuroblast NB1-1 SoxNGA1192 SoxNU6-35 neuroblast NB2-1 SoxNGA1192 neuroblast NB2-2 SoxNGA1192 neuroblast NB2-4 SoxNGA1192 SoxNU6-35 neuroblast NB2-5 SoxNGA1192 SoxNU6-35 neuroblast NB3-1 SoxNGA1192 neuroblast NB3-2 SoxNGA1192 neuroblast NB3-3 SoxNGA1192 SoxNU6-35 neuroblast NB3-5 SoxNGA1192 SoxNU6-35 neuroblast NB4-1 SoxNGA1192 neuroblast NB4-2 SoxNGA1192 neuroblast NB4-3 SoxNGA1192 neuroblast NB4-4 SoxNGA1192 SoxNU6-35 neuroblast NB5-1 SoxNGA1192 neuroblast NB5-2 SoxNGA1192 SoxNU6-35 neuroblast NB5-3 SoxNC2139 SoxNGA1192 SoxNU6-35 neuroblast NB5-4 SoxNGA1192 neuroblast NB5-5 SoxNGA1192 neuroblast NB5-6 SoxNGA1192 SoxNU6-35 neuroblast NB6-1 SoxNGA1192 neuroblast NB6-2 SoxNGA1192 neuroblast NB6-4 SoxNGA1192 SoxNU6-35 neuroblast NB7-1 SoxNU6-35 neuroblast NB7-2 SoxNGA1192 neuroblast NB7-3 SoxNGA1192 SoxNU6-35 neuroblast NB7-4 SoxNGA1192 SoxNU6-35 pCC neuron SoxNGA1192 posterior commissure SoxNGA1192 posterior commissure, with Scer\GAL4da.G32 SoxNK439.Scer\UAS posterior commissure, with Scer\GAL4elav.PLu SoxNK439.Scer\UAS RP2 motor neuron SoxNGA1192 SoxNU6-35 stage 1 neuroblast SoxNGA1192 SoxNU6-35 stage 2 neuroblast SoxNGA1192 stage 3 neuroblast SoxNGA1192 stage 4 neuroblast SoxNGA1192 stage 5 neuroblast SoxNGA1192 thorax, with Scer\GAL4unspecified SoxNScer\UAS.cBa U neuron SoxNU6-35 wing, with Scer\GAL4unspecified SoxNScer\UAS.cBa
Classical Alleles ( 6 )
For All Classical Alleles Show
Allele of SoxN Class Mutagen Stocks Known lesion SoxNNC14 1 Yes SoxNC463 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes SoxNGA1192 amorphic allele - genetic evidence ethyl methanesulfonate 0 Yes SoxNU6-35 amorphic allele - genetic evidence chemical 0 Yes SoxNC2139 hypomorphic allele - genetic evidence ethyl methanesulfonate 0 -- SoxNunspecified 0 --
Alleles Carried on Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Allele of SoxN Class Mutagen Stocks Known lesion SoxNGD4415 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes SoxNJF02018 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes SoxNScer\UAS.cOa in vitro construct - regulatory fusion 1 Yes SoxNAct5C.PB in vitro construct - regulatory fusion 0 Yes SoxNAct5C.T:Ivir\HA1.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes SoxNdsRNA.cIa in vitro construct - RNAi 0 Yes SoxNK439.Scer\UAS antimorphic allele - genetic evidence in vitro construct - regulatory fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes SoxNK439R.Act5C.T:Ivir\HA1.T:Zzzz\FLAG in vitro construct - regulatory fusion in vitro construct - coding region fusion in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement 0 Yes SoxNNIG.18024R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes SoxNScer\UAS.cBa in vitro construct - regulatory fusion 0 Yes SoxNScer\UAS.T:Avic\GFP-YFP.Venus in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2L)Exel7040 (Ryder, 2004.4.26) Df(2L)N22-5 (Overton et al., 2002)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4415} NA P{NIG.18024R} NA P{TRiP.JF02018} NA P{UAS-SoxN.B} NA P{UAS-SoxN.K439R} NA P{UAS-SoxN.O} NA P{UAS-SoxN.YFP} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 11 unique terms )
Terms Based on Experimental Evidence ( 9 terms )
Molecular Function
CV term Evidence References
chromatin DNA binding inferred from direct assay (Girard et al., 2006) protein binding inferred from physical interaction with SNCF (Bonneaud et al., 2003) RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity inferred from direct assay (Blanco et al., 2005)
Biological Process
CV term Evidence References
axon guidance inferred from mutant phenotype (Girard et al., 2006) central nervous system development inferred from mutant phenotype (Savare et al., 2005) nervous system development inferred from mutant phenotype (Buescher et al., 2002, Overton et al., 2002) positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Blanco et al., 2005) regulation of Wnt receptor signaling pathway inferred from mutant phenotype (Chao et al., 2007)
Cellular Component
CV term Evidence References
nucleus inferred from direct assay (Savare et al., 2005)
Terms Based on Predictions or Assertions ( 3 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:Q9Y651 (FlyBase, 1992-)
Biological Process
CV term Evidence References
regulation of transcription, DNA-dependent inferred from sequence or structural similarity with UniProtKB:Q9Y651 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:Q9Y651 (FlyBase, 1992-)
Sequence Ontology: Class of Gene
	gene_with_stop_codon_read_through (Jungreis, 2011.11.18) nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
SoxN - CG10077 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - CG10306 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - CG3689 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - CG5642 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - CG9769 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - Int6 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - Tango7 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - qkr58E-3 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) SoxN - α-Spec 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 SoxN allele Gene References SoxNC463 ind (Buescher et al., 2002) SoxNC2139 vnd (Buescher et al., 2002) SoxNGA1192 D (Buescher et al., 2002) SoxNU6-35 D (Overton et al., 2002) unspecified beat-Ia (Girard et al., 2006) lola (Girard et al., 2006) tup (Girard et al., 2006) Ubx (Girard et al., 2006)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 68939 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0029123 DroID - A comprehensive database of gene and protein interactions. • FBgn0029123 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 44275
Orthologs
OrthoDB Orthologs (9) - 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 EOG60GDBG Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Orthologs in Drosophila Species (EOG60GDBG)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\SoxN     Drosophila simulans   Dsim\GD23563 Y   Drosophila sechellia   Dsec\GM17140 Y   Drosophila erecta   Dere\GG25303 Y   Drosophila yakuba   Dyak\GE18794 Y   Drosophila ananassae   Dana\GF15546 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA14769 Y   Drosophila persimilis   Dper\GL25564 Y   Drosophila willistoni   Dwil\GK24531 Y
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD23563 Drosophila sechellia Dsec\GM17140 Drosophila erecta Dere\GG25303 Drosophila yakuba Dyak\GE18794 Drosophila ananassae Dana\GF15546 Drosophila pseudoobscura pseudoobscura Dpse\GA14769 Drosophila persimilis Dper\GL25564 Drosophila willistoni Dwil\GK24531 Drosophila virilis Dvir\GJ18351 Drosophila mojavensis Dmoj\GI17415 Drosophila grimshawi Dgri\GH13864
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
Bloomington	25996 y1 v1; P{TRiP.JF02018}attP2 9937 w*; KrIf-1/CyO; P{UAS-SoxN.O}3 9938 dpov1 SoxNNC14 pr1 cn1/CyO
VDRC	v41079 w1118; P{GD4415}v41079
Genomic Clones ( 1 )
	BACR01O16 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 42 )
	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	LD44245
Other clones	DPiM_LD44245
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE37363 RH18247 RH30120 RH34932 RH59527 RH61081
Other clones	12759 15017 16323 29785 30292 38707 45445 47477 57788 57932 72422 82624 122403 124060 214467.8 CK01.17B.H12 CK01.41B.A8 CK01.54D.C6 CK01.106B.G9 CK01.121B.B8 EK044443 EK088627 EK114449 EK118334 EK127723 EK139525 EK161428 EK175547 EK178624 EK180229 EK216141 EK246738 EP14305 RH17493
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0029123 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 44275
Antibody Information
	polyclonal (Buescher et al., 2002)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: SoxN CG18024 (FlyBase, 1996-) Source for merge of: SoxN Sry-rDM64 (FlyBase, 1996-)
Additional comments	Source for merge of SoxN CG18024 was sequence comparison (date:000607). (FlyBase, 1996-)
Other Comments
	The sumoylation of the SoxN product regulates its activity in vivo. (Savare et al., 2005) One of 42 Drosophila genes identified as being most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to human Mental Retardation disorders. (Inlow and Restifo, 2004) SoxN is required for the formation of the neuroblasts in the central nervous system. SoxN and D appear to be partially functionally redundant with respect to formation of ventral and intermediate neuroblasts. (Buescher et al., 2002) Loss of function mutations in SoxN result in a severe reduction in neuroblasts in the lateral and intermediate regions of the central nervous system, whereas ventral neuroblast formation is almost normal. (Buescher et al., 2002) SoxN is required for the formation of both early and late forming neuroblasts in the intermediate and lateral columns of the developing central nervous system. D and SoxN have differential and redundant functions during central nervous system development. (Overton et al., 2002)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079996 NM_001273340 RefSeq (Proteins) • NP_524735 NP_001260269 DDBJ / EMBL / GenBank • AAA28475 AAF52712 AAN71269 AGB92805 AI512383 AJ252124 AW943710 BI611307 BT001514 CAB64386 M86334 Entrez Gene - A searchable database of RefSeq genes. • 44275 UniProtKB/TrEMBL • Q9U1H5 Q9VLH8
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • High mobility group (HMG) box domain (IPR009071) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • LD44245
Linkouts
	BioGRID - A database of protein and genetic interactions • 68939 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0029123 DroID - A comprehensive database of gene and protein interactions. • FBgn0029123 DRSC - Results from RNAi screens. • FBgn0029123 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0029123 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG18024-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0029123 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 44275 Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /hjmuller/soxneur1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 44275 modMine - Data generated by the modENCODE project. • FBgn0029123
Synonyms & Secondary IDs ( 13 )
Reported As
Symbol Synonym	CG18024 (Cremazy et al., 2001, Perkins et al., 1.15.2009) DM64 (Laudet et al., 1993, Picardo, 1992, Soullier et al., 1999, ) SOX29F (Bowles et al., 2000) Sox B1 (Cremazy et al., 2001) SOXB1 (Bowles et al., 2000) soxN (Jasper et al., 2002) SoxN (Bejsovec, 2007.3.20, Bejsovec et al., 2007, Wheeler et al., 2006, Chao et al., 2007, Seibert et al., 2007, Sessa and Bianchi, 2007, Zeitlinger et al., 2007, Savare et al., 2005, Stathopoulos and Levine, 2005, Girard et al., 2006, Buescher and Chia, 2008, Seibert et al., 2008, Overton et al., 2007, Jungreis, 2011.11.18, Firth and Baker, 2007, Stagg et al., 2011, Girardot et al., 2006, Kantorovitz et al., 2009, McKimmie et al., 2005, Eivers et al., 2009, Colomb et al., 2008, Burgler and Macdonald, 2005, Kazemian et al., 2010, Bejsovec and Chao, 2012, Lloret-Llinares et al., 2012, Zhai et al., 2011, Japanese National Institute of Genetics, 2012.5.21) Sry-rDM64
Name Synonym	soxneuro (Buescher et al., 2002) SoxNeuro (Girad, 1999.12.21, Wheeler et al., 2006, Chao et al., 2007, Savare et al., 2005, Girard et al., 2006, Buescher and Chia, 2008, Overton et al., 2007, Firth and Baker, 2007, Carpenter et al., 2009, Eivers et al., 2009, Hong et al., 2012) Sox-neuro (Bejsovec et al., 2006, Bejsovec et al., 2007, Chao et al., 2007) Sox-Neuro (Sharma and Nirenberg, 2007, Zhai et al., 2011) Sry-related DM64
Secondary FlyBase IDs
	FBgn0010277 FBgn0032070
References ( 67 )
Generate a list of	All references relating to this gene ( 67 )
List References by type	Research paper  ( 36 ) Supplementary material  ( 3 ) Review  ( 3 ) Personal communication to FlyBase  ( 8 ) Abstract  ( 9 ) FlyBase analysis  ( 2 ) DNA/RNA sequence record  ( 2 ) Stock list  ( 1 ) Website  ( 1 ) Curated genome annotation  ( 2 )
Recent research papers ( 7 )
	Bejsovec and Chao, 2012, Development 139(4): 690--698 crinkled reveals a new role for Wingless signaling in Drosophila denticle formation. [FBrf0217282] Fisher et al., 2012, Proc. Natl. Acad. Sci. U.S.A. 109(52): 21330--21335 DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. [FBrf0220344] Hong et al., 2012, G3 (Bethesda) 2(8): 873--882 Microarray-Based Capture of Novel Expressed Cell Type-Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster. [FBrf0219214] Junion et al., 2012, Cell 148(3): 473--486 A transcription factor collective defines cardiac cell fate and reflects lineage history. [FBrf0217404] Lloret-Llinares et al., 2012, Nucleic Acids Res. 40(19): 9493--9505 dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes. [FBrf0219748] Stagg et al., 2011, Development 138(11): 2171--2183 Dual role for Drosophila lethal of scute in CNS midline precursor formation and dopaminergic neuron and motoneuron cell fate. [FBrf0213671] Zhai et al., 2011, Biochem. Biophys. Res. Commun. 414(4): 761--766 Functional dissection of the Hox protein Abdominal-B in Drosophila cell culture. [FBrf0216579] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...