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Table 4 Conserved motifs in salmon 3'UTRs

From: Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

No

Motifs1

Observed2

Genomic3

Random seq4

Reverse5

p-value6

miRNA/protein7

1

ATGTTTT

127, 109

48

39 +/- 6

55

39.2

 

2

AATGTTT

118, 99

40

36 +/- 4

57

34.4

miR-543

3

TACTGTA

90, 85

31

20 +/- 6

30

45.2

miR-101, miR-199, miR-144

4

TAAATGT

80, 75

42

32 +/- 4

37

19.4

 

5

ATGTATT

89, 73

27

34 +/- 5

34

16.1

miR-466b-3-3p

6

TGTAAAT

79, 72

39

33 +/- 5

30

16.2

PUF

7

TTGTAAA

79, 68

29

31 +/- 6

46

15.4

PUF

8

TTGTATT

70, 60

23

37 +/- 7

28

6.0

CFI

9

AATGTAT

83, 64

28

28 +/- 4

33

15.6

CFI

10

TGTCTGT

76, 63

27

16 +/- 6

41

30.6

 

11

TGTCATT

70, 61

37

24 +/- 4

37

17.6

miR-425-5, miR-731, miR-489

  1. 1Sequence of common 7-mers in the 3'UTRs,
  2. 2Total number of times the motif was observed in 3'UTRs, number of 3'UTR sequences with the motif
  3. 3Number of times the motif was observed in salmon genomic DNA (from BAC sequence DQ156149)
  4. 4Mean number of times the motif was observed in ten separate shuffling trials along with standard deviation
  5. 5Number of times the motif was observed on the reverse strand of the 3'UTRs
  6. 6Chi-square p-value using a 2 × 2 contingency table as described in methods
  7. 7miRNAs or proteins known to bind 3'UTR target sequences identical to the motif
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BMC Genomics

ISSN: 1471-2164

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