Table 3 |
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|
Filtering of smORFs with evidence of translation |
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|
Pipeline filters |
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|
|
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|
Gene name [reference] |
Length (codons) |
tBLASTn E-value (pass if < 10-3) |
Ka/Ks (pass if < 0.1) |
Syntenic to D. pseudoobscura |
RNASeq overlaps (pass if > 1) |
|
|
|||||
|
Akh [63] |
79 |
2e-22 |
0.04 |
False |
12 |
|
CG13551 [64] |
87 |
6e-14 |
0.18 |
False |
12 |
|
CG14235 [64] |
96 |
5e-42 |
0.06 |
True |
12 |
|
CG17127 [64] |
98 |
4e-42 |
0.05 |
True |
10 |
|
CG30415 [65] |
82 |
4e-36 |
0.05 |
False |
12 |
|
CG32039 [64] |
82 |
1e-15 |
0.06 |
False |
12 |
|
81 |
6e-23 |
0.05 |
True |
12 |
|
|
Cype [65] |
77 |
8e-26 |
0.18 |
True |
12 |
|
Dbi [64] |
86 |
7e-39 |
0.48 |
True |
4 |
|
Dro [66] |
64 |
4e-17 |
0.32 |
True |
9 |
|
Drs [66] |
70 |
NA |
NA |
Na |
9 |
|
IM1 [66] |
45 |
1e-12 |
0.09 |
True |
9 |
|
45 |
9e-14 |
0.00 |
True |
9 |
|
|
42 |
0.075 |
0.11 |
False |
12 |
|
|
99 |
3e-45 |
0.00 |
True |
10 |
|
|
Mtk [66] |
52 |
7e-11 |
0.27 |
True |
12 |
|
Nplp2 [63] |
86 |
8.4 |
0.07 |
False |
11 |
|
Nplp3 [63] |
90 |
1e-10 |
0.14 |
False |
7 |
|
Nplp4 [63] |
64 |
NA |
NA |
NA |
12 |
|
RpL38 [67] |
70 |
8e-34 |
0.00 |
False |
8 |
|
RpS21 [67] |
83 |
8e-36 |
0.02 |
True |
12 |
|
RpS27 [67] |
84 |
2e-44 |
0.00 |
False |
12 |
|
65 |
6e-23 |
0.00 |
True |
12 |
|
|
smt3 [64] |
90 |
2e-47 |
0.00 |
False |
12 |
|
sun [64] |
61 |
1e-16 |
0.16 |
True |
12 |
|
Number of smORFs passing each pipeline filter (out of a total of 25) |
21 |
15 |
13 |
25 |
|
|
|
|||||
|
Filtering of previously annotated smORFs with proteomics evidence of translation. References cited in the first column include evidence of translation for each of these smORFs. Entries in bold do not pass the corresponding filter. Ka/Ks, ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitution; NA, not available. |
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|
Ladoukakis et al. Genome Biology 2011 12:R118 doi:10.1186/gb-2011-12-11-r118 |
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