Table 1.
microRNA/target pairs predicted by MovingTargets using the following strict targeting criteria: minimum 3 target sites, maximum dG of microRNA/target hybridization of -15 kcal/mole at RT for each target site, minimum 7 out of 8 consecutive base pairs in microRNA 5' end, maximum 1 G:U base pair in microRNA 5' region. Transcription factor targets are listed first followed by neural targets. Gene function and biological process are as given by FlyBase http://www.flybase.net, March 2004.
| Target | miRNA | # target sites | dG of miRNA-mRNA hybrid (kcal/mole) | Molecular Function | Biological process |
| CrebA |
mir-92b mir-312 |
3 4 |
-16, -24, -19 -16, -20, -17, -22 |
transcription factor | salivary gland development |
| fkh | mir-315 | 3 | -18, -16, -17 | transcription factor | salivary gland morphogenesis |
| Eip74EF | mir-34 | 3 | -25, -27, -21 | transcription factor | mesoderm development |
| Eip93FA | mir-280A | 3 | -21, -15, -16 | transcription factor | autophagy, induction of apoptosis by hormones |
| pros | mir-34 | 3 | -18, -17, -18 | transcription factor | ectoderm development |
| zfh1 | mir-5 | 3 | -17, -15, -15 | transcription factor | ectoderm development, mesoderm development |
| zfh2 | mir-276a-3 | 3 | -16, -15, -17 | transcription factor, RNA binding | ectoderm development |
| SoxN |
mir-34 mir-309 |
3 3 |
-23, -24, -16 -19, -16, -20 |
transcription factor, DNA bending | ectoderm development, visual perception |
| HLHm5 | mir-7 | 3 | -24, -24, -26 | transcription factor | ectoderm development, cell proliferation |
| CG32527B | mir-34 | 3 | -25, -24, -21 | multiple (including transcription factor) | unknown |
| ab | let-7 | 5 | -20, -25, -17, -17, -19 | transcription factor | transmission of nerve impulse, sex determination |
| sbb | mir-33 | 3 | -16, -17, -19 | transcription factor | axon guidance, axon target recognition, larval walking behavior |
| nerfin-1 |
mir-279 mir-286 |
3 3 |
-19, -17, -24 -19, -16, -27 |
transcription factor | neuronal lineage restriction |
| Syn | mir-92b | 3 | -19, -20, -15 | unknown | neurotransmitter secretion, synaptic vesicle exocytois |
| synaptogyrin | mir-313 | 3 | -17, -16, -15 | unknown | synaptic vesicle exocytosis, regulation of calcium ion dependent exocytosis |
| Pkc98E | mir-210 | 3 | -15, -15, -15 | multiple | multiple (including neural processes) |
| nAcRbeta-96A | mir-210 | 3 | -19, -18, -23 | nicotinic acetylcholine-activated cation-selective channel activity, acetylcholine receptor activity | multiple (including neural processes) |
| WA |
bantam mir-280A |
4 3 |
-21, -16, -27, -17 -17, -19, -15 |
unknown | induction of apoptosis, programmed cell death |
| kel |
mir-310 mir-311 mir-312 |
3 4 4 |
-20, -19, -22 -17, -21, -19, -15 -16, -18, -20, -17 |
actin binding | apoptosis, ovarian ring canal formation |
| RhoGEF2 | mir-9c | 3 | -16, -16, -18 | Rho guanyl-nucleotide exchange factor activity, diacylglycerol binding | multiple |
| adat |
mir-3 mir-309 mir-318 |
3 3 3 |
-28, -17, -19 -23, -16, -15 -26, -15, -20 |
tRNA specific adenosine deaminase activity | purine base metabolism |
| bru-2 |
mir-9a mir-9c |
3 3 |
-19, -17, -16 -19, -15, -16 |
RNA binding | mRNA processing, protein metabolism |
| CG32062A |
mir-12 mir-280A |
4 3 |
-19, -17, -23, -15 -16, -16, -19 |
RNA binding | unknown |
| fus | mir-303 | 3 | -16, -15, -16 | RNA binding | epidermal growth factor receptor signaling pathway |
| mblA | mir-280A | 3 | -17, -17, -21 | RNA binding, DNA binding | mesoderm development |
| Asph | mir-9b | 3 | -21, -19, -16 | peptide-aspartate beta-dioxygenase activity | transmembrane receptor protein tyrosine kinase signaling pathway |
| CG32429 | mir-33 | 3 | -17, -17, -18 | unknown | unknown |
| lmg | mir-34 | 3 | -27, -20, -22 | unknown | mitotic anaphase |
| wb | mir-34 | 4 | -22, -22, -19, -23 | binding, structural molecule activity | cell-cell adhesion, cell-matrix adhesion, signal transduction |
| Cbl | mir-34 | 3 | -22, -17, -22 | ligase activity | cellular defense response |
| Pdi |
mir-34 mir-263b mir-305 mir-316 |
4 3 4 3 |
-26, -23, -30, -20 -18, -15, -17 -24, -18, -19, -22 -21, -16, -21 |
protein disulfide isomerase activity | protein folding, protein modification |
| CG31637 | mir-92b | 3 | -17, -18, -17 | sulfotransferase activity | carbohydrate metabolism |
| CG3689 | mir-210 | 3 | -20, -15, -17 | pre-mRNA splicing factor activity | mRNA cleavage, nuclear mRNA splicing, via spliceosome |
| CG8475 | mir-263b | 3 | -18, -17, -21 | kinase activator activity, phosphorylase kinase regulator activity | glycogen metabolism |
| didum | mir-276a-3 | 3 | -18, -16, -15 | multiple | multiple |
| Ggamma1 | mir-277 | 3 | -19, -16, -15 | heterotrimeric G-protein GTPase activity | G-protein coupled receptor protein signaling pathway |
| CG1441 | mir-278 | 3 | -30, -22, -26 | oxidoreductase activity | unknown |
| Rh6 | mir-278 | 3 | -19, -22, -20 | G-protein coupled photoreceptor activity | phototransduction, visual perception, sensory perception |
| CG31163A | mir-289A | 3 | -17, -15, -17 | SH3/SH2 adaptor protein activity | unknown |
| CG18854 | mir-306-3 | 4 | -27, -19, -24, -21 | inositol-triphosphate 3-kinase activity | unknown |
| CG7908 | mir-309 | 3 | -17, -19, -22 | zinc ion binding, metalloendopeptidase avtivity | cell surface receptor linked signal transduction, proteolysis and petidolysis |
| CG14507 |
mir-276a-5 mir-276b-5 |
3 3 |
-24, -20, -21 -24, -20, -21 |
phospholipase A2 activity | unknown |
| CG33085A,B |
mir-184-3 mir-284A |
3 3 |
-21, -22, -16 -23, -25, -17 |
argininosuccinate lyase activity | unknown |
| CG32316B |
mir-184-3 mir-278 |
3 3 |
-20, -22, -16 -18, -20, -23 |
oxoglutarate dehydrogenase (succinyl-transferring) activity | tricarboxylic acid cycle |
| CG32912B | mir-279 | 3 | -15, -21, -16 | peptidoglycan recognition activity | immune response |
| CG33047A,B |
mir-133 mir-284A |
3 3 |
-19, -17, -19 -27, -17, -15 |
alpha-L-fucosidase activity | O-glycoside catabolism, fucose metabolism |
| CG33075B | mir-306-3 | 3 | -26, -20, -27 | carrier activity | transport |
| CG32956B |
mir-9a mir-9b mir-9c mir-33 |
5 5 5 3 |
-17, -19, -18, -21, -18 -17, -20, -16, -20, -17 -17, -22, -18, -20, -18 -19, -23, -18 |
multiple | multiple |
| CG33038B |
mir-9a mir-9b mir-9c |
4 5 4 |
-20, -17, -16, -18 -18, -19, -17, -16, -16 -21, -17, -17, -19 |
multiple | heparan sulfate proteoglycan biosynthesis, proton transport |
| CG32791 | mir-31a | 3 | -15, -17, -15 | unknown | multiple |
| tinc | mir-34 | 3 | -22, -23, -33 | unknown | unknown |
| CG9932 | mir-263b | 4 | -16, -21, -20, -21 | unknown | unknown |
| CG30389 |
mir-14 mir-34 |
3 3 |
-17, -16, -25 -28, -21, -24 |
unknown | unknown |
| CG3975 | mir-33 | 3 | -17, -19, -22 | unknown | unknown |
| CG8963 | mir-6 | 3 | -16, -17, -17 | unknown | unknown |
| CG3638 | mir-184-3 | 3 | -27, -17, -22 | unknown | unknown |
| CG33006B | mir-278 | 3 | -20, -15, -23 | unknown | unknown |
| CG31305B | mir-278 | 4 | -16, -32, -29, -25 | multiple | unknown |
| CG32206A | mir-289A | 3 | -15, -15, -16 | unknown | unknown |
| CG12071 | mir-305 | 3 | -17, -21, -19 | unknown | unknown |
A: exact 5' and 3' ends for mir-263a, mir-274, mir-280, mir-282, mir-284, mir-289 have not yet been determined (6); target predictions for these microRNAs are likely to change once the precise microRNA sequences are known
B: gene annotated as a "gene cassette"; molecular function and biological process listed is the union of molecular functions and biological processes for each ORF in the putative dicistronic transcript