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Gene Dmel\so

General Information
Symbol	Dmel\so	Species	D. melanogaster
Name	sine oculis	Annotation symbol	CG11121
Feature type	protein_coding_gene	FlyBase ID	FBgn0003460
Gene Model Status	Current	Stock availability	15 publicly available
Also Known As	Drl, mda
Genomic Location
Chromosome (arm)	2R	Recombination map	2-57.1
Cytogenetic map	43B3-43C1	Sequence location	2R:3,306,537..3,322,377 [+]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene sine oculis is referred to in FlyBase by the symbol Dmel\so (CG11121, FBgn0003460). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding; transcription factor binding; sequence-specific DNA binding; sequence-specific distal enhancer binding RNA polymerase II transcription factor activity. There is experimental evidence that it is involved in the biological process: entrainment of circadian clock; ring gland development; positive regulation of transcription from RNA polymerase II promoter; glial cell migration; circadian rhythm; optic lobe placode formation; compound eye morphogenesis; spermatogenesis; Bolwig's organ morphogenesis. 55 alleles are reported. The phenotypes of these alleles are annotated with: organ system subdivision; nervous system; multi-cell-component structure; adult segment; external compound sense organ; peripheral nervous system; adult brain; presumptive embryonic/larval nervous system; primordium; larval head segment. It has one annotated transcript and one annotated polypeptide. Protein features are: Homeobox; Homeobox, conserved site; Homeodomain-like; Homeodomain-related. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed within 00-18 hour embryonic stages, at stages throughout the pupal period. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult eye. Comments on Affy2 ProbeSet: ProbeSet 1641675_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of so. Gene sequence location is 2R:3306537..3322377.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	so: sine oculis (J.C. Hall) Ocelli always absent; eyes usually reduced to small groups of ommatidia, and occasionally missing; eye field sometimes in form of an eye stalk protruding from head with an irregular arrangement of ommatidia; heavy ommatidial disruption with many receptor cells missing. Optic lobes reduced in size, and many flies have no lamina. The reduced volume of adult optic lobes is due to accentuated degeneration of precursor neurons that occurs to a certain degree in normal pupal development (Fischbach, 1983); the increased severity in the mutant includes degeneration of axons in second optic chiasma (Fischbach and Technau, 1984); sol enhances this kind of degeneration, but acts on a separate set of precursors for columnar visual system neurons--as confirmed by anatomical analysis of sol; so double mutant, which ends up with tiny, rudimentary optic lobes (Fischbach and Technau, 1984); sol; so also leads to a central brain that is smaller than normal due to missing afferents from visual system (Fischbach and Technau, 1984); more specifically, there is a reduction in number of axons in anterior optic track in so, and combining so with sol causes a further reduction, but again, these two genes act independently on separate subsets of such axons (Fischbach and Lyly-Hunerberg, 1983). Histological studies reveal that the eye-antenna disc in third-instar larvae appears normal until differentiation begins, at which time cell death is observed (Hofbauer and Campos-Ortega). More extreme at elevated temperatures; lethal at 30; temperature-sensitive period for eye defect in third instar. Survival sensitive to elevated temperature at all developmental stages (Ransom, 1980, DIS 55: 126). Mosaic studies demonstrate that so acts in developing eye tissue and that the resulting reduction in retinal innervation leads to death of cells in the lamina and breakdown of medulla and lobula-complex neuropil (Fischback and Technau). Nonphototactic (Benzer, 1967, Proc. Nat. Acad. Sci. USA 58: 1112-19) and visual orientation almost absent (Bulthoff, 1982, DIS 58: 31). Studies of circadian rhythms in so show eclosion to be normally periodic (Engelmann and Honneger, 1966); adult activity rhythms are robust, in that so, even when thoroughly eyeless, responds to light:dark cues such that it entrains to these conditions (is periodically active vs. inactive, and anticipates the environmental transitions) and subsequently free-runs with obvious circadian periodicities in constant darkness (Helfrich and Engelmann, 1983; Dushay, Rosbash, and Hall, 1989); however, these behavioral rhythms are frequently aberrant, e.g., with "split" active components appearing after several days of free-run and with dual periodicities extractable from the locomotor data (Helfrich, 1986); nearly all adults are dual-period when so combined with sol (Helfrich, 1986). soD Heterozygote has very small glazed eyes; more extreme than Drmio/+;soD/+/+ has a very clear phenotype, but weaker than that of Drmio/+ (i.e., about the size of Gla/+, but not glazed). Heterozygote has excellent viability; homozygous lethal.
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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FB2011_10	References Park et al., 2011, PLoS Genet. 7(8): e1002241
FB2012_01	References Levine et al., 1997, Dev. Dynamics 209(1): 1--14 Sequence features HFA07693 BKN28128 Controlled Vocabulary Terms positive regulation of transcription from RNA polymerase II promoter transcription factor binding sequence-specific distal enhancer binding RNA polymerase II transcription factor activity
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 43B3-43C1   Limits computationally determined from genome sequence between P{lacW}cosk16101 and P{EP}CG1600EP398
Experimentally Determined Cytological Location
Cytogenetic map Notes References 43C1-43C1   (determined by in situ hybridisation)   (Cheyette et al., 1994) 43C-43C   (determined by in situ hybridisation)   (Murphy and O'Tousa, 1991)
Experimentally Determined Recombination Data
Location	2-57.1   2-51 (Craymer, 1984)
Left of (cM)	amos (Craymer, 1984)
Right of (cM)	amos (Heitzler et al., 1993)
Notes	1 or 2cM to the left of amos. (Craymer, 1984)
Gene Model & Products
Please see the GBrowse view of Dmel\so for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) so-RA FBtr0088970  NM_057385   3104   416
Additional Transcript Data & Comments
Reported size (kB)	2.8 (northern blot) (Cheyette et al., 1994)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein so-PA   FBpp0089177   45.0   416   8.82     NP_476733   AAF59260
Additional Polypeptide Data & Comments
Reported size (kDa)	416 (aa); 45 (kD predicted) (Serikaku and O'Tousa, 1994) 416 (aa) (Cheyette et al., 1994)
Comments	A 63 amino acid peptide from the so protein was identified as sufficient for specific DNA binding. (Hazbun et al., 1997)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE013599 AAF59260   AC005452   AI135343   AI292757   AI292783   AI389439   AI404112   AI405714   AW941814   AY060309 AAL25348   BF495769   BF502538   BI487026   BI487053   BI487107   BI579676   BT029256   CO190014   CO190063   CO268083   CO275970   CO276423   CO276778   CO280518   CO342817   CZ476910   EC059550   EC060031   EC060179   EC061842   EC073866   EC197533   EC220670   EC254792   EC260531   EL871612   L31626 AAA21800   L31627   S77459 AAB34685   Z50344
UniProtKB/Swiss-Prot	Q27350
UniProtKB/TrEMBL	Q95T66
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 protein binding site FBsf0000160404 2R:3,318,622..3,318,650 bound_moiety=toy-XP evidence=experimental bound_moiety=ey-XP (Punzo et al., 2002, Bergman et al., 2004) protein binding site FBsf0000160405 2R:3,318,834..3,318,856 bound_moiety=toy-XP evidence=experimental (Bergman et al., 2004, Punzo et al., 2002) protein binding site FBsf0000160406 2R:3,318,916..3,318,946 bound_moiety=toy-XP evidence=experimental bound_moiety=ey-XP (Bergman et al., 2004, Punzo et al., 2002) protein binding site FBsf0000160407 2R:3,318,797..3,318,818 bound_moiety=toy-XP evidence=experimental (Bergman et al., 2004, Punzo et al., 2002) protein binding site FBsf0000160408 2R:3,318,749..3,318,778 evidence=experimental bound_moiety=toy-XP bound_moiety=ey-XP (Bergman et al., 2004, Punzo et al., 2002)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic optic lobe primordium   (Cheyette et al., 1994) embryonic stage 5 -- 6   organism | anterior   (Seimiya and Gehring, 2000) Comment:anterior ring embryonic stage 6   visual primordium   (Seimiya and Gehring, 2000) embryonic stage 6 -- 7   embryonic optic lobe primordium   (De Velasco et al., 2004) stomatogastric nervous system anlage   (De Velasco et al., 2004) ventral furrow | anterior & restricted   (De Velasco et al., 2004) embryonic stage 9   optic lobe | presumptive   (Serikaku and O'Tousa, 1994) embryonic stage 11   embryonic labral segment   (Seimiya and Gehring, 2000) embryonic stage 11 -- 16   embryonic epidermis | segment boundary   (Seimiya and Gehring, 2000) embryonic stage 12   epidermis   (Serikaku and O'Tousa, 1994) embryonic stage 16   Bolwig organ   (Serikaku and O'Tousa, 1994) third instar larval stage   eye disc   (Cheyette et al., 1994) late third instar larval stage   eye disc anterior to the morphogenetic furrow   (Seimiya and Gehring, 2000) eye disc posterior to the morphogenetic furrow   (Seimiya and Gehring, 2000) morphogenetic furrow   (Seimiya and Gehring, 2000) ventral thoracic disc | restricted   (Seimiya and Gehring, 2000)
Additional Descriptive Data
	Embryonic stage 6-7 expression of so is observed in the anlages of the optic lobe and the stomatogastric nervous system, and at the anterior lip of the ventral furrow. (De Velasco et al., 2004) Blastoderm expression is posterior to that of Optix. (Seimiya and Gehring, 2000)
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage   embryonic optic lobe primordium   (Cheyette et al., 1994) embryonic stage 9   optic lobe | presumptive   (Serikaku and O'Tousa, 1994) embryonic stage 12   epidermis   (Serikaku and O'Tousa, 1994) embryonic stage 16   Bolwig organ   (Serikaku and O'Tousa, 1994) third instar larval stage   photoreceptor cell R1 -- photoreceptor cell R7   (Serikaku and O'Tousa, 1994) eye-antennal disc   (Serikaku and O'Tousa, 1994) adult stage | male   cyst cell   • nucleus (Fabrizio et al., 2003) adult stage   optic lobe   (Serikaku and O'Tousa, 1994) ocellus   (Serikaku and O'Tousa, 1994) photoreceptor cell R1 -- photoreceptor cell R7   (Serikaku and O'Tousa, 1994) western blot Stage Tissue/Position (including subcellular localization) Reference third instar larval stage   eye disc   (Cheyette et al., 1994)
Additional Descriptive Data
	so protein can be detected in mid to late stage spermatogonial cyst cells. (Fabrizio et al., 2003) so protein is first detected in the eye disc at the onset of the third instar at which time it is expressed in a gradient increasing from anterior to posterior. so protein continues to be expressed in the third instar and is found in nuclei anterior to, within, and posterior to the morphogenetic furrow. It is expressed in most if not all cells of the disc epithelium. so protein is also expressed in the optic lobe primordium in embryos starting in stage 5. (Cheyette et al., 1994) so protein isexpressed in the optic lobe primordia immediately anterior to the cephalicfurrow and in cells just anterior to the stomodeal invagination at stage9. In stage 12, so protein is detected bilaterally at segmentalboundaries in a set of unidentified epidermal cells. At stage 16,expression is limited to four bilaterally positioned organs that arethought to be Bolwig\'s organs. In eye discs, so protein is detected innuclei on both sides of the morphogenetic furrow. It is found inundifferentiated cells of the eye disc epithelium ahead of the furrow andwithin individual photoreceptor cell clusters posterior to the furrow.R1-6 are more heavily stained than R7. In the adult eye, so proteinlocalizes to photoreceptor cells. It is also detected in adults in nucleiof the optic lobes and ocelli. (Serikaku and O'Tousa, 1994)
Marker for
Subcellular Localization
CV Term	nucleus (Serikaku and O'Tousa, 1994)
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data for FBgn0003460    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0003460 Very low expression bin max 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 moderate expression to a trough of very low expression. Peak expression observed within 00-18 hour embryonic stages, at stages throughout the pupal period. [download data (TSV)] Guide to modENCODE expression level colors   No expression (0 - 0)   Extremely low expression (1 - 10)   Very low expression (11 - 100)   Low expression (101 - 400)   Moderate expression (401 - 1400)   Moderately high expression (1401 - 4000)   High expression (4001 - 10000)   Very high expression (10001 - 100000)   Extremely high expression (100001 - 2000000) Linear, scaled to maximum FBgn0003460 expression level Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr  (168) embryo 04-06hr  (468) embryo 06-08hr  (688) embryo 08-10hr  (1009) embryo 10-12hr  (1056) embryo 12-14hr  (892) embryo 14-16hr  (990) embryo 16-18hr  (707) embryo 18-20hr  (390) embryo 20-22hr  (210) embryo 22-24hr  (195) larva L1  (240) larva L2  (200) larva L3 12hr old  (205) larva L3 puffstage 1-2  (198) larva L3 puffstage 3-6  (296) larva L3 puffstage 7-9  (317) white prepupae new  (284) white prepupae 12hr  (464) white prepupae 24hr  (617) pupae 2d postWPP  (477) pupae 3d postWPP  (367) pupae 4d postWPP  (315) adult male 01day  (320) adult male 05day  (369) adult male 30day  (309) adult female 01day  (174) adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0003460 expression level Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr  (168) embryo 04-06hr  (468) embryo 06-08hr  (688) embryo 08-10hr  (1009) embryo 10-12hr  (1056) embryo 12-14hr  (892) embryo 14-16hr  (990) embryo 16-18hr  (707) embryo 18-20hr  (390) embryo 20-22hr  (210) embryo 22-24hr  (195) larva L1  (240) larva L2  (200) larva L3 12hr old  (205) larva L3 puffstage 1-2  (198) larva L3 puffstage 3-6  (296) larva L3 puffstage 7-9  (317) white prepupae new  (284) white prepupae 12hr  (464) white prepupae 24hr  (617) pupae 2d postWPP  (477) pupae 3d postWPP  (367) pupae 4d postWPP  (315) adult male 01day  (320) adult male 05day  (369) adult male 30day  (309) adult female 01day  (174) adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    44 embryo 02-04hr    168 embryo 04-06hr    468 embryo 06-08hr    688 embryo 08-10hr    1009 embryo 10-12hr    1056 embryo 12-14hr    892 embryo 14-16hr    990 embryo 16-18hr    707 embryo 18-20hr    390 embryo 20-22hr    210 embryo 22-24hr    195 larva L1    240 larva L2    200 larva L3 12hr old    205 larva L3 puffstage 1-2    198 larva L3 puffstage 3-6    296 larva L3 puffstage 7-9    317 white prepupae new    284 white prepupae 12hr    464 white prepupae 24hr    617 pupae 2d postWPP    477 pupae 3d postWPP    367 pupae 4d postWPP    315 adult male 01day    320 adult male 05day    369 adult male 30day    309 adult female 01day    174 adult female 05day    69 adult female 30day    70 Expression Level Scale  None   Extremely low   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     FlyAtlas Anatomical Expression Data for FBgn0003460    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0003460 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult eye. [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 (1000 - 25000) Linear, scaled to maximum FBgn0003460 expression level Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0003460 expression level Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    32.575 Larval Midgut no informative data Larval Hindgut    26.2 Larval Malpighian Tubules    2.3 Larval Fat Body    7.9 Larval Salivary Gland    3.9 Larval Trachea    7.025 Larval Carcass    56.15 Adult Head    52.5 Adult Eye    159.4 Adult Brain    9.5 Adult Thoracic-Abdominal Ganglion    3.8 Adult Crop    58.7 Adult Midgut no informative data Adult Hindgut    21.6 Adult Malpighian Tubules    4.2 Adult Fat Body    4.3 Adult Salivary Gland    9.4 Adult Heart    41.125 Adult VirginFemale Spermatheca    6.6 Adult InseminatedFemale Spermatheca    6.8 Adult Ovary    4.9 Adult Testis    67.2 Adult Male Accessory Gland    9.6 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut no informative data 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 no informative data 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 no informative data FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    52.5   NA  Eye    159.4   NA  Brain    9.5   32.575  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    3.8   NA  Crop    58.7   no informative data  Midgut    no informative data   26.2  Hindgut    21.6   2.3  Malpighian Tubules    4.2   7.9  Fat Body    4.3   3.9  Salivary Gland    9.4   NA  Heart    41.125   7.025  Trachea    NA   NA  VirginFemale Spermatheca    6.6   NA  InseminatedFemale Spermatheca    6.8   NA  Ovary    4.9   NA  Testis    67.2   NA  Male Accessory Gland    9.6   56.15  Carcass    no informative data modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_11
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003460 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG11121-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for so 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 soD lethal, with Scer\GAL4pnr-MD237 soGD1537 lethal | embryonic stage (with so3) soD lethal | embryonic stage (with soD) so3 lethal | embryonic stage | recessive so3 so8 lethal | first instar larval stage | recessive soD lethal | recessive soD viable so1 so5 so7 so9 so10 soSKE-1 viable (with so3) so9 viable (with so9) so3 Sterility Allele fertile | male (with so3) so9 fertile | male (with so9) so3 Other Phenotypes Allele behavior defective | larval stage | recessive somda cell growth defective | somatic clone so1 so3 circadian rhythm defective so1 increased cell death so1 neuroanatomy defective so1 so3 somda neuroanatomy defective | embryonic stage | recessive sounspecified phototaxis behavior defective somda size defective, with Scer\GAL4ey.PU soScer\UAS.cPa visible so1 so5 so9 so10 soSKE-1 visible, with Scer\GAL4dpp.blk1 soScer\UAS.cPa visible, with Scer\GAL4ey.PH soScer\UAS.cPa visible, with Scer\GAL4ey.PU soScer\UAS.cPa visible | dominant soD visible | recessive so1 so+2 visual behavior defective so1 soDrv4 soDrv10 soDrv11 soDrv14 wild-type sohs.PA sohs.PC Phenotype manifest in Allele Bolwig organ so1 so10 so3 so5 so7 so8 so9 somda corpus cardiacum primordium so3 cortex of medulla so1 sounspecified cuticle | ectopic | somatic clone so1 embryonic/larval optic stalk so1 embryonic/larval stomatogastric nervous system so3 embryonic stomatogastric nervous system so3 eye so1 so10 so5 so9 soD soDrv31 soDrv6 soDrv8 sounspecified soSKE-1 eye, with Scer\GAL4dpp.blk1 soScer\UAS.cPa eye, with Scer\GAL4ey.PH soG201D.Scer\UAS soScer\UAS.cPa soV200D.Scer\UAS eye, with Scer\GAL4ey.PU soScer\UAS.cPa eye | cell non-autonomous | somatic clone so3 eye | heat sensitive soAD.hs soV200D.hs sohs.PA eye | heat sensitive, with Scer\GAL4hs.PB soV200D.Scer\UAS eye | somatic clone so1 eye disc so1 eye disc, with Scer\GAL4ey.PH soG201D.Scer\UAS soV200D.Scer\UAS eye disc & neuron so9 eye disc | somatic clone so1 so3 eye photoreceptor cell so1 glial cell & larval optic lobe so1 interfollicle cell so3 lamina so1 sounspecified lamina & neuron so1 lamina | precursor sounspecified lamina anlage glial cell so1 so5 larval LN period neuron somda lobula sounspecified medulla sounspecified medulla neuropil so1 morphogenetic furrow | somatic clone so1 so3 neuroblast & embryonic optic lobe primordium sounspecified ocellus so+2 so1 so9 soDrv10 soDrv11 soDrv14 soDrv31 soDrv4 soDrv6 soDrv8 soSKE-1 ommatidium so1 so5 ommatidium, with Scer\GAL4dpp.blk1 soScer\UAS.cPa ommatidium, with Scer\GAL4ey.PH soScer\UAS.cPa optic chiasm sounspecified optic lobe so1 somda sounspecified P5m fiber tract founder cluster sounspecified Pdf neuron so1 photoreceptor cell somda sounspecified photoreceptor cell | larval stage soD photoreceptor cell R1 | somatic clone so3 photoreceptor cell R6 | somatic clone so3 photoreceptor cell R7 | somatic clone so3 retina so1 subretinal glial cell so1 so5 visual primordium so1 so10 so3 so5 so7 so8 so9 somda
Classical Alleles ( 38 )
For All Classical Alleles Show
Allele of so Class Mutagen Stocks Known lesion so1 loss of function allele spontaneous 2 Yes sod09734 P-element activity 2 -- soD antimorphic allele - genetic evidence, gain of function allele ethyl nitrosourea 2 Yes so3 amorphic allele - genetic evidence, loss of function allele ethyl methanesulfonate 1 Yes so+2 hypomorphic allele - genetic evidence spontaneous 1 -- soMB12256 1 -- soNP1543 1 -- so8 amorphic allele - genetic evidence P-element activity 0 Yes so10 loss of function allele P-element activity 0 Yes so11 0 -- so13 0 -- so45j natural population 0 -- so4 ethyl methanesulfonate 0 -- so5 loss of function allele, hypomorphic allele - genetic evidence ethyl methanesulfonate 0 Yes so6 ethyl methanesulfonate 0 -- so7.GAL4 gene conversion 0 Yes so7 loss of function allele P-element activity 0 Yes so9 loss of function allele, hypomorphic allele - genetic evidence P-element activity 0 Yes soDrv10 X ray 0 -- soDrv11 X ray 0 -- soDrv13 X ray 0 -- soDrv14 X ray 0 -- soDrv1 X ray 0 -- soDrv23 0 -- soDrv27 X ray 0 -- soDrv29 X ray 0 -- soDrv2 X ray 0 -- soDrv31 X ray 0 -- soDrv3 X ray 0 -- soDrv4 X ray 0 -- soDrv6 X ray 0 -- soDrv8 X ray 0 -- soL31 0 -- somda P-element activity 0 Yes soold 0 -- soSHE-7 ethyl methanesulfonate 0 Yes soSKE-1 ethyl methanesulfonate 0 Yes sounspecified spontaneous 0 --
Alleles Carried on Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Allele of so Class Mutagen Stocks Known lesion soGD1537 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes soHMS01441 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes soJF02201 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes soKK108128 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes soScer\UAS.cPa in vitro construct - regulatory fusion 1 Yes soAD.hs in vitro construct - amino acid replacement 0 Yes soD200.P257.Scer\UAS in vitro construct - amino acid replacement 0 Yes soG201D.Scer\UAS in vitro construct - amino acid replacement 0 Yes soG66A.hs in vitro construct - amino acid replacement 0 Yes sohs.PA in vitro construct - regulatory fusion 0 Yes sohs.PC in vitro construct - regulatory fusion 0 Yes soL257P.Scer\UAS in vitro construct - amino acid replacement 0 Yes soMtnA.T:Hsap\MYC in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes soso10-soAE.hs in vitro construct - regulatory fusion 0 Yes soso11-soAE in vitro construct - regulatory fusion 0 Yes soV200D.hs in vitro construct - amino acid replacement 0 Yes soV200D.Scer\UAS in vitro construct - amino acid replacement 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2R)BSC263 (Christensen and Cook, 2007.3.22) Df(2R)BSC264 (Christensen and Cook, 2007.3.22) Df(2R)cn3 (Yannopoulos et al., 1981) Df(2R)cn9 (Yannopoulos et al., 1981) Df(2R)cn15 (Yannopoulos et al., 1981) Df(2R)cn16 (Yannopoulos et al., 1981) Df(2R)cn-S5 (Heitzler et al., 1993) Df(2R)Drlrv3 (Heitzler et al., 1993) Df(2R)Drlrv5 (Heitzler et al., 1993) Df(2R)Drlrv7 (Heitzler et al., 1993) Df(2R)Drlrv15 (Heitzler et al., 1993) Df(2R)Drlrv17 (Heitzler et al., 1993) Df(2R)Drlrv18 (Heitzler et al., 1993) Df(2R)Drlrv20 (Heitzler et al., 1993) Df(2R)Drlrv21 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)Drlrv22 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)Drlrv24 (Heitzler et al., 1993) Df(2R)Drlrv25 (Heitzler et al., 1993) Df(2R)Drlrv26 (Heitzler et al., 1993) Df(2R)Drlrv28 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)Drlrv30 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)NCX9 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)NCX11 (Heitzler et al., 1993) Df(2R)Npk-rv1 (Roote and Ashburner, 2005.6) Df(2R)sple-D2 (Heitzler et al., 1993) Df(2R)sple-D3 (Heitzler et al., 1993) Df(2R)sple-J1 (Heitzler et al., 1993) Df(2R)sple-J2 (Heitzler et al., 1993) Df(2R)sple-N3 (Heitzler et al., 1993) Df(2R)ST1 (Ashburner et al., 1981)
Not disrupted in	Df(2R)cn8 (Yannopoulos et al., 1981) Df(2R)cn10 (Yannopoulos et al., 1981) Df(2R)cn17 (Yannopoulos et al., 1981) Df(2R)cn-S6 (Heitzler et al., 1993) Df(2R)cn-S8 (Heitzler et al., 1993) Df(2R)cos-2 (Heitzler et al., 1993) Df(2R)cos-3 (Heitzler et al., 1993) Df(2R)DX1 (Heitzler et al., 1993) Df(2R)DX14 (Heitzler et al., 1993) Df(2R)EW60 (Heitzler et al., 1993) Df(2R)H23 (Heitzler et al., 1993) Df(2R)nap2 (Heitzler et al., 1993) Df(2R)NCX5 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)NCX8 (Heitzler et al., 1993) Df(2R)NCX10 (Heitzler et al., 1993) Df(2R)NCX13 (Heitzler et al., 1993, Serikaku and O'Tousa, 1994) Df(2R)Npk-rv2 (Roote and Ashburner, 2005.6) Df(2R)pk-N5 (Heitzler et al., 1993) Df(2R)pwn5 (Heitzler et al., 1993) Df(2R)sple-D1 (Heitzler et al., 1993) Df(2R)tor-rx6 (Heitzler et al., 1993) In(2R)cn10 (Yannopoulos et al., 1981)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD1537} NA P{KK108128} NA P{TRiP.HMS01441} NA P{TRiP.JF02201} NA P{UAS-so.D200.P257} NA P{UAS-so.G201D} NA P{UAS-so.L257P} NA P{UAS-so.P} NA P{UAS-so.V200D} NA heat-shock construct P{hsp70/so} NA P{hsp-so} NA P{hs-so.AD} NA P{hs-so.G66A} NA P{hs-so.V200D} NA P{so10-soAE-hsp70-so} NA reporter construct P{so7-lacZ} No P{so9-lacZ} No P{so-lacZ.5} No P{so-lacZ.10.27bp} No P{so-lacZ.10.EY/TOYmt.1.2.5} No P{so-lacZ.10.EY+TOYmt.1-5} No P{so-lacZ.10.TOYmt} No P{so-lacZ.10} No P{toy-lacZ.EEP} No characterization construct P{so7-GAL4.EY/TOYmt.1.2.5} NA P{so7-GAL4.EY+TOYmt.1-5} NA P{so7-GAL4.TOYmt} NA P{so7-GAL4} NA P{so10-GAL4.EY/TOYmt.1.2.5} NA P{so10-GAL4.EY+TOYmt.1-5} NA P{so10-GAL4.TOYmt} NA P{so10-GAL4} NA P{so11-soAE-so} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{XP}sod09734 NA insertion of enhancer trap binary system Mi{ET1}soMB12256 No P{GawB}so7.GAL4 No P{GawB}soNP1543 No insertion of enhancer trap P{A92}so7 No miscellaneous insertions P{?'A92}so9 NA P{?'A92}so10 NA P{ninaE+}somda NA
Gene Ontology: Function, Process & Cellular Component ( 18 unique terms )
Terms Based on Experimental Evidence ( 13 terms )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with ey (Zhang et al., 2006) inferred from physical interaction with Sobp (Kenyon et al., 2005) sequence-specific distal enhancer binding RNA polymerase II transcription factor activity inferred from direct assay (Yan et al., 2003) sequence-specific DNA binding inferred from direct assay (Kenyon et al., 2005) inferred from mutant phenotype (Zhang et al., 2006) transcription factor binding inferred from physical interaction with eya (Kenyon et al., 2005) inferred from physical interaction with gro (Kenyon et al., 2005)
Biological Process
CV term Evidence References
Bolwig's organ morphogenesis inferred from mutant phenotype (Suzuki and Saigo, 2000) circadian rhythm inferred from genetic interaction with mnb (Helfrich, 1986) compound eye morphogenesis inferred from mutant phenotype (Kenyon et al., 2005) entrainment of circadian clock inferred from mutant phenotype (Helfrich-Forster et al., 2002) glial cell migration inferred from mutant phenotype (Hummel et al., 2002) optic lobe placode formation inferred from mutant phenotype (Daniel et al., 1999) positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Kenyon et al., 2005) inferred from mutant phenotype (Yan et al., 2003) ring gland development inferred from mutant phenotype (De Velasco et al., 2004) spermatogenesis inferred from mutant phenotype (Fabrizio et al., 2003)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity traceable author statement (Martini et al., 2000, Gibson and Schubiger, 2001)
Biological Process
CV term Evidence References
compound eye development non-traceable author statement (Swiss-Prot Project Members, 1997.2.1) eye-antennal disc morphogenesis traceable author statement (Martini et al., 2000) regulation of transcription, DNA-dependent inferred from sequence or structural similarity with UniProtKB:Q62231 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with mouse Six2 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1997.2.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions so allele Gene References so1 cry (Helfrich-Forster et al., 2002) ey (Halder et al., 1998) gish (Hummel et al., 2002) gl (Helfrich-Forster et al., 2002) tsh (Pan and Rubin, 1998) so3 ey (Pignoni, 2001.1.26) eya (Hsiao et al., 2001) so5 gish (Hummel et al., 2002) soD nej (Kumar et al., 2004) soScer\UAS.cPa dpp (Curtiss and Mlodzik, 2000) eya (Bui et al., 2000) unspecified eya (Pignoni et al., 1997, Fabrizio et al., 2003) grim (Mueller et al., 2005) Psn (Mahoney et al., 2006) rpr (Mueller et al., 2005) W (Mueller et al., 2005)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 61542 DroID - A comprehensive database of gene and protein interactions. • FBgn0003460 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35662
Orthologs
Genome-wide drosophilid orthologs	Dana\GF12955 Dere\GG23277 Dgri\GH21164 Dmoj\GI18759 Dper\GL11165 Dpse\GA10770 Dsec\GM20951 Dvir\GJ21783 Dwil\GK21318 Dyak\GE19124
Curated drosophilid orthologs	Dmon\so (Kankare et al., 2010) Dpse\GA10770
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • AAEL009170-PA Aedes aegypti (mosquito) AGAP011695-PA Anopheles gambiae (mosquito) At1g19700.1 Arabidopsis thaliana (wall cress) 84947 Branchiostoma floridae (lancelet) ENSBTAP00000016104 Bos taurus (bovine) ENSCAFP00000022966 Canis familiaris (dog) CAGL0H02959g Candida glabrata (haploid yeast) ENSCINP00000029084 Ciona intestinalis (sea squirt) ENSCPOP00000014020 Cavia porcellus (guinea pig) ENSCSAVP00000004408 Ciona savignyi (sedentary tunicate) 180303 Capitella spl (polychaete worm) 107399 Daphnia pulex (daphnia) ENSDARP00000028379 Danio rerio (zebra fish) ENSECAP00000020329 Equus caballus (horse) ENSGACP00000011147 Gymnopilus aculeatus (mushroom) ENSGALP00000036574 Gallus gallus (chicken) 181629 Hypsipyla robusta (cedar shoot borer) ENSP00000247182 Homo sapiens (human) KLLA0B10450g Kluyveromyces lactis (yeast) ENSMODP00000010746 Monodelphis domestica (gray opossum) ENSMMUP00000024349 Macaca mulatta (rhesus monkey) ENSMUSP00000059026 Mus musculus (house mouse) XP_001600428.1 Nasonia vitripennis (wasp) ENSOANP00000008462 Ornithorynchus anatinus (platypus) ENSORLP00000019739 Oryzias latipes (japanese killifish) LOC_Os06g01934.1 Oryza sativa (asian rice) PHUM003768-PA Pediculus humanus (human body louse) ENSPPYP00000006675 Pongo pygmaeus (orangutan) ENSPTRP00000010878 Pan troglodytes (chimpanzee) ENSRNOP00000037345 Rattus norvegicus (norway rat) 4807299 Sorghum bicolor (sorghum) Smp_039470 Schistosoma mansoni (trematode parasite) XP_001181583.1 Strongylocentrotus purpuratus (purple sea urchin) XP_972167.2 Tribolium castaneum (red flour beetle) ENSTNIP00000020483 Tetraodon nigroviridis (green spotted pufferfish) 268351 Thalassiosira pseudonana (marine diatom) ENSTRUP00000026932 Takifugu rubripes (pufferfish Takifugu) ENSXETP00000036917 Xenopus tropicalis (frog) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV12377 NV11287 LH12334 LH17942 ISCW007609 FBgn0236530 FBgn0236484 FBgn0225128 FBgn0223310 FBgn0209239 FBgn0208901 FBgn0182304 FBgn0175882 FBgn0175832 JGI_V11_107399 JGI_V11_14338 FBgn0074967 FBgn0070826 FBgn0149092 FBgn0148775 FBgn0142085 FBgn0141498 FBgn0025360 FBgn0129360 FBgn0128626 FBgn0115477 FBgn0115428 FBgn0090684 FBgn0089989 CPIJ018547 BGIBMGA011285 ACYPI001400 ACYPI000853 GB16761 GB15213 AGAP011695 AGAP003871 AAEL014151 AAEL009170 AAEL000414 PB23222 PB25940 PHUM338410 PHUM515180 GLEAN_00361 TC030468
Stocks & Reagents
Stocks Listed in FlyBase ( 15 )
Bloomington	401 so1 4287 soD/CyO 26808 w*; P{UAS-so.P}1 29286 w1118; Mi{ET1}soMB12256 19319 w1118; P{XP}sod09734/CyO 31912 y1 v1; P{TRiP.JF02201}attP2 8874 Dp(?;2)bwD, so3 bwD/CyO
Harvard	- P{XP}sod09734
Kyoto	105892 so1 107671 soD/CyO
VDRC	v104386 P{KK108128}VIE-260B v8950 w1118; P{GD1537}v8950
	More stocks available...
Genomic Clones ( 2 )
	BACR04G20 BACR26B18 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 31 )
	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	GH15741
Other clones	FI01103
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT09424 AT18203 GH13034 GH15773 GH20614 GH23712 GH25830 RE70531 RE70558 RE70617 RE73743
Other clones	653 8026 40047 53258 214277.3 214351.12 CK01.118D.F1 CK01.145A.H2 CK01.147C.E3 EK046001 EK046301 EK090121 EK119261 EK120818 EK122032 EK154247 EP15548 IP03690
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0003460 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35662
Antibody Information
	polyclonal (Cheyette et al., 1994, Serikaku and O'Tousa, 1994)
Other Information
Discoverer
	Milani, 1939.
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	The following allelic combinations have an increasingly severe eye phenotype, in which the size of the adult eye is reduced until it is lost completely: so5/so9 < so9/so9 < so9/so3 < so1/so1. (Kenyon et al., 2005) The consensus sequence GTAANYNGANAYC/G is necessary for so binding to DNA. (Pauli et al., 2005) RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells. (Boutros et al., 2004) Mutant embryos lack the corpus cardiacum and stomatogastric nervous system. (De Velasco et al., 2004) gish, so, ey and hh act in the posterior region of the eye disc to prevent precocious glial cell migration. (Hummel et al., 2002) Bolwig's organ formation is governed by ato, the expression of which is under the control of hh, eya and so. (Suzuki and Saigo, 2000) so and eya are two mediators of the eye inducing activity of ey. ey appears to induce the initial expression of so and eya in the eye disc. so and eya then participate in a positive feedback loop that regulates the expression of all three genes. In the embryonic head, however, so acts in parallel to ey and toy. The epistatic relationships among the corresponding vertebrate homologs are very similar to those observed in Drosophila. (Halder et al., 1998) so and eya regulate common steps in eye development including cell proliferation, patterning and neuronal development. (Pignoni et al., 1997) Molecular and developmental analysis reveals so encodes a homeodomain-containing protein that is expressed and required in the unpatterned epithelium prior to morphogenesis. Analysis of mosaic clones supported an essential developmental role for so in eye development. (Cheyette et al., 1994) The mutant phenotype demonstrates the homeodomain containing so gene product is involved in the specification of the larval and adult visual system development during embryogenesis. (Serikaku and O'Tousa, 1994) Observations of mutants support the proposal that axon fascicles can make at least some pathfinding decisions independently of their neighbours. (Kunes et al., 1993) Mutants of so display a degraded ERG response. Eye development is also abnormal having structural defects within the rhabdomeres of the photoreceptor cells. (Murphy and O'Tousa, 1991) In tests of locomotor activity rhythms, singly mutant mnb adults are basically normal, but a high proportion of mnb so double mutants show complex rhythmicities (dual circadian periodicities) with about 20% being arrhythmic (3 times greater than wild type). (Helfrich, 1986)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057385 RefSeq (Proteins) • NP_476733 DDBJ / EMBL / GenBank • AAA21800 AAB34685 AAF59260 AAL25348 AC005452 AI292757 AW941814 AY060309 CZ476910 L31626 L31627 S77459 Z50344 Entrez Gene - A searchable database of RefSeq genes. • 35662 UniProtKB/Swiss-Prot • Q27350 UniProtKB/TrEMBL • Q95T66
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287)
Linkouts
	BioGRID - A database of protein and genetic interactions • 61542 DroID - A comprehensive database of gene and protein interactions. • FBgn0003460 DRSC - Results from RNAi screens. • FBgn0003460 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003460 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG11121-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0003460 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 35662 InParanoid A subset of ortholog calls from InParanoid. • AAEL009170-PA Aedes aegypti (mosquito) AGAP011695-PA Anopheles gambiae (mosquito) At1g19700.1 Arabidopsis thaliana (wall cress) 84947 Branchiostoma floridae (lancelet) ENSBTAP00000016104 Bos taurus (bovine) ENSCAFP00000022966 Canis familiaris (dog) CAGL0H02959g Candida glabrata (haploid yeast) ENSCINP00000029084 Ciona intestinalis (sea squirt) ENSCPOP00000014020 Cavia porcellus (guinea pig) ENSCSAVP00000004408 Ciona savignyi (sedentary tunicate) 180303 Capitella spl (polychaete worm) 107399 Daphnia pulex (daphnia) ENSDARP00000028379 Danio rerio (zebra fish) ENSECAP00000020329 Equus caballus (horse) ENSGACP00000011147 Gymnopilus aculeatus (mushroom) ENSGALP00000036574 Gallus gallus (chicken) 181629 Hypsipyla robusta (cedar shoot borer) ENSP00000247182 Homo sapiens (human) KLLA0B10450g Kluyveromyces lactis (yeast) ENSMODP00000010746 Monodelphis domestica (gray opossum) ENSMMUP00000024349 Macaca mulatta (rhesus monkey) ENSMUSP00000059026 Mus musculus (house mouse) XP_001600428.1 Nasonia vitripennis (wasp) ENSOANP00000008462 Ornithorynchus anatinus (platypus) ENSORLP00000019739 Oryzias latipes (japanese killifish) LOC_Os06g01934.1 Oryza sativa (asian rice) PHUM003768-PA Pediculus humanus (human body louse) ENSPPYP00000006675 Pongo pygmaeus (orangutan) ENSPTRP00000010878 Pan troglodytes (chimpanzee) ENSRNOP00000037345 Rattus norvegicus (norway rat) 4807299 Sorghum bicolor (sorghum) Smp_039470 Schistosoma mansoni (trematode parasite) XP_001181583.1 Strongylocentrotus purpuratus (purple sea urchin) XP_972167.2 Tribolium castaneum (red flour beetle) ENSTNIP00000020483 Tetraodon nigroviridis (green spotted pufferfish) 268351 Thalassiosira pseudonana (marine diatom) ENSTRUP00000026932 Takifugu rubripes (pufferfish Takifugu) ENSXETP00000036917 Xenopus tropicalis (frog) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /neural/sineocul.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 35662 modMine - Data generated by the modENCODE project. • FBgn0003460 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV12377 NV11287 LH12334 LH17942 ISCW007609 FBgn0236530 FBgn0236484 FBgn0225128 FBgn0223310 FBgn0209239 FBgn0208901 FBgn0182304 FBgn0175882 FBgn0175832 JGI_V11_107399 JGI_V11_14338 FBgn0074967 FBgn0070826 FBgn0149092 FBgn0148775 FBgn0142085 FBgn0141498 FBgn0025360 FBgn0129360 FBgn0128626 FBgn0115477 FBgn0115428 FBgn0090684 FBgn0089989 CPIJ018547 BGIBMGA011285 ACYPI001400 ACYPI000853 GB16761 GB15213 AGAP011695 AGAP003871 AAEL014151 AAEL009170 AAEL000414 PB23222 PB25940 PHUM338410 PHUM515180 GLEAN_00361 TC030468 REDfly - A database of transcriptional regulatory elements. • FBgn0003460
Synonyms & Secondary IDs ( 21 )
Reported As
Symbol Synonym	ami   CG11121 (Keleman et al., 2009.8.5, Perkins et al., 2009, Ni et al., 2011.7.19) Drl (MacIver et al., 1998, Craymer, 1984, Heitzler et al., 1993, ) mda (Murphy and O'Tousa, 1993, Murphy and O'Tousa, 1991, ) Mdu (Sanchez-Elsner et al., 2006) med   old   So (Silver et al., 2003, Kenyon et al., 2001, Zhang et al., 2006, Rogers et al., 2005, Morillo et al., 2008, Wrobel et al., 2008, Li et al., 2008, Firth and Baker, 2009) so (Yang et al., 2005, Fabrizio et al., 2003, Kumar and Luhur, 2007, Kumar and Salzer, 2007, Kumar and Datta, 2007, Kumar and Weasner, 2007, Kumar and Henderson, 2007, Christensen and Cook, 2007.3.22, Christensen and Cook, 2007.3.22, Wang and Montell, 2005, Mahoney et al., 2006, Kwon and Montell, 2006, Wang and Montell, 2006, Roederer et al., 2005, Fic et al., 2007, Zordan et al., 2001, Togane et al., 2007, Garcia-Murillas et al., 2006, Anderson et al., 2006, Friedrich, 2006, Aerts et al., 2007, Yoshii et al., 2004, Silver et al., 2003, Murakami et al., 2007, Weasner and Kumar, 2009, Wang et al., 2008, Salzer and Kumar, 2008, Henderson and Kumar, 2008, Tarone et al., 2008, Weasner and Kumar, 2008, Anderson and Kumar, 2008, Chang et al., 2003, Wang et al., 2007, Hayashi et al., 2008, Weasner et al., 2007, Jemc and Rebay, 2007, Tanaka-Matakatsu and Du, 2008, Yao et al., 2008, Levine et al., 1997, Salzer and Kumar, 2009, Curtiss et al., 2007, Braid and Verheyen, 2008, Liu et al., 2009, Schuettengruber et al., 2009, Yoshii et al., 2009, Punzo et al., 2004, McNabb and Truman, 2008, de Velasco et al., 2007, Zeitlinger et al., 2007, Ostrin et al., 2006, Salzer et al., 2010, Salzer and Kumar, 2010, Voolstra et al., 2010, Wülbeck et al., 2008, Blanco et al., 2010, Aerts et al., 2010, Oros et al., 2010, Brockmann et al., 2011, Chang et al., 2010, Park et al., 2011) SO (Jemc and Rebay, 2007) somda (Serikaku, 1995.8.25)
Name Synonym	absent minded   Droplet   medusa (Murphy and O'Tousa, 1991, ) Medusa (Sanchez-Elsner et al., 2006) optic lobe defective   sine oculis (Fabrizio et al., 2003, Kumar and Luhur, 2007, Kumar and Salzer, 2007, Kumar and Datta, 2007, Kumar and Weasner, 2007, Kumar and Henderson, 2007, Han et al., 2006, Wang and Montell, 2006, Roederer et al., 2005, Zordan et al., 2001, Silver et al., 2003, Murakami et al., 2007, Weasner and Kumar, 2009, Wang et al., 2008, Pereanu and Hartenstein, 2006, Wang et al., 2007, Coiffier et al., 2008, Weasner et al., 2007, Tanaka-Matakatsu and Du, 2008, Liu et al., 2009, Schuettengruber et al., 2009, Yoshii et al., 2009, McNabb and Truman, 2008, Ostrin et al., 2006, Salzer et al., 2010, Wülbeck et al., 2008, Blanco et al., 2010, Oros et al., 2010, Chang et al., 2010, Park et al., 2011) Sine oculis (Zhang et al., 2006, Rogers et al., 2005, Morillo et al., 2008, Jemc and Rebay, 2007) Sine Oculis (Jemc and Rebay, 2007, Li et al., 2008, Salzer and Kumar, 2010) sine oculus (Fernald, 2006) sinus oculis (Voolstra et al., 2010)
Secondary FlyBase IDs
	FBgn0004392 FBgn0004874
References ( 317 )
Generate a list of	All references relating to this gene ( 317 )
List References by type	Research paper  ( 172 ) Supplementary material  ( 5 ) Review  ( 47 ) Erratum  ( 1 ) Personal communication to FlyBase  ( 13 ) Abstract  ( 68 ) FlyBase analysis  ( 3 ) DNA/RNA sequence record  ( 1 ) Protein sequence record  ( 1 ) Computer file  ( 3 ) Automatic genome annotation  ( 1 ) Curated genome annotation  ( 1 ) Stock list  ( 1 )
Recent research papers ( 11 )
	Brockmann et al., 2011, Dev. Dyn. 240(1): 75--85 Regulation of ocellar specification and size by twin of eyeless and homothorax. [FBrf0212641] Park et al., 2011, PLoS Genet. 7(8): e1002241 Specification of Drosophila corpora cardiaca neuroendocrine cells from mesoderm is regulated by Notch signaling. [FBrf0215231] Aerts et al., 2010, PLoS Biol. 8(7): e1000435 Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification. [FBrf0211419] Blanco et al., 2010, Dev. Biol. 344(2): 1088--1099 Genetic interactions of eyes absent, twin of eyeless and orthodenticle regulate sine oculis expression during ocellar development in Drosophila. [FBrf0211396] Chang et al., 2010, Brain Res. 1324: 1--13 Hedgehog-dependent down-regulation of the tumor suppressor, vitamin D3 up-regulated protein 1 (VDUP1), precedes lamina development in Drosophila. [FBrf0210439] Hoang et al., 2010, Dev. Dyn. 239(9): 2367--2385 Drosophila CtBP regulates proliferation and differentiation of eye precursors and complexes with Eyeless, Dachshund, Dan, and Danr during eye and antennal development. [FBrf0211770] Kankare et al., 2010, BMC Ecol. 10(1): 3 Changes in gene expression linked with adult reproductive diapause in a northern malt fly species: a candidate gene microarray study. [FBrf0210028] Oros et al., 2010, Dev. Biol. 346(2): 258--271 Dorsal eye selector pannier (pnr) suppresses the eye fate to define dorsal margin of the Drosophila eye. [FBrf0211877] Salzer et al., 2010, Genetics 184(1): 185--197 The retinal determination gene eyes absent is regulated by the EGF receptor pathway throughout development in Drosophila. [FBrf0209690] Salzer and Kumar, 2010, PLoS ONE 5(1): e8510 Identification of retinal transformation hot spots in developing Drosophila epithelia. [FBrf0209699] Voolstra et al., 2010, J. Biol. Chem. 285(3): 2130--2139 NinaB is essential for Drosophila vision but induces retinal degeneration in opsin-deficient photoreceptors. [FBrf0209707] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...