Table 3

Filtering of smORFs with evidence of translation

Pipeline filters


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

CG3321 [64,65]

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

IM2 [63,66]

45

9e-14

0.00

True

9

IM4 [63,66]

42

0.075

0.11

False

12

l(2)06225 [64,65]

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

RpS28b [64,65]

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.

Ladoukakis et al. Genome Biology 2011 12:R118   doi:10.1186/gb-2011-12-11-r118

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