Summary of gene functions, Ty3 intermediate phenotypes, and transposition phenotypes for 66 mutants. Based on GO functions, a subset of 66 genes identified in the current Ty3 screen representing nine categories from Table 1: stress/chaperone, cytoskeletal, vesicular/vacuolar, RNA processing, unknown, translation, Ty1 transposition repressors, nuclear transport, and DNA maintenance were chosen for analysis of transposition intermediates (Fun). Transposition frequencies (Tpn) are indicated only as increased (red) or decreased (green). Gag3 was monitored by Western blot analysis, described in the Methods, of two independent transformants induced for expression of wild-type Ty3 for 24 h. Analysis used anti-CA and anti-IN (not shown in this figure). Gag3 species were considered increased (red, 4 or 5), decreased (green, 1 or 2) or the same as wild type (black, 3) on the same gel using PGK as a loading control (Supplemental Fig. 1). This analysis is qualitative rather than quantitative. Ty3 cDNA was monitored and quantified by Southern blot analysis, as described in the Methods, using a probe to the internal domain of Ty3 (Supplemental Fig. 1). The amount of Ty3 cDNA is expressed as the ratio of Ty3 cDNA to Ty3 plasmid in the same blot. The wild-type ratio was 0.57 ± 0.31. The cDNA/plasmid ratio (cDNA) was rated greater than wild type if the average ratio of two transformants was greater than wild type plus one standard deviation (red) and less than wild type if the average of two transformants was less than wild type minus one standard deviation (green). In three cases (VAM7, YOL083W, and SRO9) the measurement from one transformant was used because the second transformant did not show presence of the plasmid (Supplemental Fig. 1). Panels were sorted in Excel to show relationships of function, Gag3 protein, cDNA, and transposition frequency. Sorting priority is indicated in labels A–E. Genes are colored according to function as indicated in the legend in functional groups corresponding to those in Table 1.