Table 2

Summary of U12 introns identified in a range of eukaryotic species.

Number of ESTs analyzed

U12 spliceosomal RNAs

U12 AT-AC introns

(5' rule)

U12 GT-AG introns

(5' rule)

U2 GC-AG introns

U2 GT-AG introns

Other AT-AC introns


B

S

B

S

B

S

B

S

B

S

Trichinella spiralis

25,268

+

3 (3)

3 (3)

1 (1)

13 (8)

217

217

14697

14685

5

5

Monosiga brevicollis

29,495

-

0

0

0

1 (0)

134

134

13327

13326

10

10

Rhizopus oryzae

13,313

+

1 (1)

1 (1)

2 (2)

3 (2)

71

71

5520

5519

3

3

Phycomyces blakesleeanus

47,847

+

9 (8)

8 (8)

8 (8)

12 (10)

446

446

13504

13500

31

32

Phakopsora pachyrhizi

34,394

-?

0

0

0

1 (0)

10

10

561

560

2

2

Acanthamoeba castellanii

13,784

+

1 (0)

0

1 (1)

3 (0)

21

21

1232

1230

2

2

Entamoeba histolytica

14,388

-

0

0

0

0

0

0

160

160

4

4

Physarum polycephalum

25,393

+

83 (14)

27 (15)

88 (57)

218 (109)

34

34

6452

6326

251

307

Chlamydomonas reinhardtii

202,044

-

0

0

0

0

532

532

25053

25053

7

7

Phytophthora infestans

94,091

+

2 (2)

2 (2)

1 (1)

1 (1)

66

66

6601

6601

9

9

Phytophthora sojae

28,467

+

2 (2)

2 (2)

1 (1)

1 (1)

34

34

3351

3351

5

5

Thalassiosira pseudonana

61,913

-

0

0

0

0

37

37

5140

5140

13

13

Phaeodactylum tricornutum

133,871

-

0

0

0

0

23

23

3815

3815

7

7


Table shows prediction according to methods of Burge et al (B) and Sheth et al (S) [11]. The "5' rule" is that 5' splice site sequence is RTATCCTT where one of the Cs in positions +5 and +6 may be converted into a T. Occurrence of U12 snRNAs is from Davila-Lopez et al [8]. For sequences of U12 introns as predicted by the Burge et al method, see additional file 2.

Bartschat and Samuelsson BMC Genomics 2010 11:106   doi:10.1186/1471-2164-11-106

Open Data