TABLE 3.
Drosophila genes that are significantly up-regulated in response to Pum RNAi and contain one or more PREs
| Pum-repressed, PRE-containing gene | PRE location | |||||
|---|---|---|---|---|---|---|
| Flybase ID | Symbol | Summary | 5′ UTR | CDS | 3′ UTR | Bound |
| FBgn0000077 | amx | Neurodevelopment, Notch pathway | 0 | 0 | 2 | + |
| FBgn0001128 | gpdh1 | Glycerol-3-phosphate dehydrogenase 1, metabolism | 0 | 0 | 2 | + |
| FBgn0002973 | numb | Neurodevelopment, Notch pathway | 0 | 0 | 1 | + |
| FBgn0011704 | RnrS | Deoxynucleotide biosynthesis, ribonucleoside diphosphate reductase, small subunit | 0 | 0 | 1 | + |
| FBgn0024889 | Kap-α1 | Spermatogenesis, nuclear import, karyopherin | 0 | 0 | 1 | + |
| FBgn0024994 | Ugalt | UDP-galactose transporter | 0 | 0 | 3 | + |
| FBgn0028360 | cdc7 | Promotes DNA replication, protein kinase | 0 | 0 | 2 | + |
| FBgn0031491 | α4GT1 | α1,4-Galactosyltransferase 1, glycosphingolipid biosynthesis | 0 | 0 | 1 | + |
| FBgn0036502 | CG7841 | Function and phenotype unknown | 0 | 0 | 2 | + |
| FBgn0037110 | ORMDL | Negative regulator of sphingolipid synthesis | 0 | 0 | 2 | + |
| FBgn0039135 | CG13603 | Function and phenotype unknown | 0 | 0 | 1 | + |
| FBgn0000180 | bib | Neurodevelopment, Notch pathway | 0 | 1 | 1 | |
| FBgn0003079 | Raf | Oncogene, serine–threonine kinase | 0 | 0 | 2 | |
| FBgn0003716 | tkv | Germ cell development, TGF β receptor for dpp signaling | 0 | 0 | 3 | |
| FBgn0010473 | tutl | Neurodevelopment, axon guidance, motor control, IgG superfamily transmembrane protein | 0 | 0 | 1 | |
| FBgn0011288 | snap25 | SNARE complex, neurotransmitter release | 0 | 1 | 2 | |
| FBgn0015766 | Msr-110 | Integral membrane component, molecular function unknown, expressed in the digestive system, embryo germ band, prothoracic gland | 0 | 0 | 1 | |
| FBgn0024245 | dnt | Muscle development, cell morphogenesis, differentiation, Ryk family of Wnt receptor tyrosine kinase | 0 | 0 | 1 | |
| FBgn0025626 | CG4281 | Function unknown, expressed in the gonad and digestive system | 0 | 0 | 2 | |
| FBgn0026144 | CBP | Sarcoplasmic calcium-binding protein | 1 | 0 | 0 | |
| FBgn0031401 | papi | piRNA pathway, repression of transposable elements during meiosis | 0 | 0 | 1 | |
| FBgn0034405 | Jheh2 | Juvenile hormone epoxide hydrolase 2 | 1 | 0 | 0 | |
| FBgn0034611 | MFS16 | Integral membrane component, molecular function unknown | 0 | 0 | 2 | |
| FBgn0035696 | Best2 | Predicted chloride transport channel | 0 | 1 | 2 | |
| FBgn0038460 | CG18622 | Function and phenotype unknown | 0 | 0 | 4 | |
| FBgn0039045 | Ctns | Amino acid transmembrane transport, Cystine/H+ symporter | 0 | 0 | 1 | |
| FBgn0040334 | Tsp3A | Notch signaling, tetraspanin superfamily transmembrane protein | 0 | 0 | 1 | |
| FBgn0040348 | CG3703 | GTPase activator, expressed in embryonic brain and larval ventral nerve cord | 0 | 0 | 1 | |
| FBgn0041629 | Hexo2 | β-N-acetylglucosaminidase involved in carbohydrate metabolism | 0 | 0 | 1 | |
| FBgn0264090 | CG43759 | Function unknown | 0 | 0 | 3 | |
| FBgn0283509 | Phm | Neuropeptide biosynthesis, peptidylglycine-α-hydroxylating monooxygenase | 0 | 0 | 2 | |
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The FlyBase gene name and symbol for each gene are listed, along with a summary of its function and the location of PREs within the transcript. For genes with multiple mRNA isoforms, PRE parameters are based on the longest isoform. Genes that were also up-regulated in both Pum KO cell lines are indicated in bold text. Genes with transcripts bound by Pum in embryos, identified by RIP-seq, are indicated with a “+.”
