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FlyAtlas: the Drosophila gene expression atlas

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Biotechnology & Biological Sciences Research Council
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Latest news: FlyAtlas2 : A Database web-app for fruitfly expression with added RNA & miRNA goodness ! Click here to visit the application. Read all about it here.

This dataset was generated by Venkat Chintapalli, Jing Wang & Julian Dow at the University of Glasgow with funding from the UK's BBSRC.
It gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly?
For each gene & tissue, you're given the mRNA SIGNAL (how abundant the mRNA is), the mRNA ENRICHMENT (compared to whole flies), and the Affymetrix PRESENT CALL (out of 4 arrays, how many times it was detectably expressed).

String to look for? (e.g. vha, cell adhesion, receptor, aquaporin, adenylate, CG1147, pnt)

Searching for FBGN0003249 through 18771 annotations produced 1 hits


rhodopsin (Rh3):

Annotation Number : CG10888
FlyAtlas2 : Click Here for expression data based on RNA-Seq and or miRNA-Seq analyses
Flybase ID : FBgn0003249
Gbrowse : chr3R:15906777-15908172 (-) // 99.57 //
Probeset : 1627829_at
Accessions : protein= NP_524411;, nucleotide= NM_079687;
Pathway : UV // inferred from direct assay /// 0007604 // phototransduction
Interpro : UV // non-traceable author statement /// 0007604 // phototransduction
FlyMine data for FBgn0003249.
BDGP gene expression has embryonic in situ data for Rh3: 2 pix of staining in 1 body parts.
Homophila reports that CG10888 is a close match (5e-13) to human gene RGR (NP_002912), a gene associated with Retinitis pigmentosa, autosomal dominant (3);Retinitis pigmentosa, autosomal recessive (3).
TRiP has 3 RNAi stocks for FBgn0003249 available for purchase.
VDRC has 2 RNAi stocks for FBgn0003249 available for purchase.


TissuemRNA SignalPresent CallEnrichmentAffy Call
Brain15 ± 24 of 4 0.10Down
Head2111 ± 634 of 410.10Up
Eye5948 ± 1244 of 428.41Up
Thoracicoabdominal ganglion15 ± 13 of 4 0.10Down
Salivary gland10 ± 10 of 4 0.05Down
Crop6 ± 20 of 4 0.00Down
Midgut6 ± 10 of 4 0.00Down
Tubule5 ± 10 of 4 0.00Down
Hindgut6 ± 10 of 4 0.00Down
Heart14 ± 21 of 4 0.07Down
Fat body7 ± 40 of 4 0.04Down
Ovary3 ± 10 of 4 0.00Down
Testis4 ± 10 of 4 0.00Down
Male accessory glands11 ± 30 of 4 0.10Down
Virgin spermatheca1 ± 00 of 4 0.01Down
Mated spermatheca4 ± 10 of 4 0.02Down
Adult carcass3 ± 00 of 4 0.00Down
Larval CNS4 ± 21 of 4 0.02Down
Larval Salivary gland6 ± 10 of 4 0.03Down
Larval midgut7 ± 30 of 4 0.03Down
Larval tubule3 ± 10 of 4 0.00Down
Larval hindgut6 ± 11 of 4 0.03Down
Larval fat body9 ± 30 of 4 0.00Down
Larval trachea154 ± 2921 of 4 0.74None
Larval carcass5 ± 20 of 4 0.03Down
S2 cells (growing)3 ± 10 of 4 0.02Down
Whole fly209 ± 114 of 4

Looking for FBgn0003249. 1 entries matched from 18771, in 1 s.

Chintapalli, V. R., Wang, J. and Dow, J. A. T. (2007). Using FlyAtlas to identify better Drosophila models of human disease. Nature Genetics 39: 715-720

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